International Journal of Molecular Sciences

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5 pages, 193 KiB

Open AccessEditorial

Evolution and Function of the Chloroplast. Current Investigations and Perspectives

by Bartolomé Sabater

Int. J. Mol. Sci. 2018, 19(10), 3095; https://doi.org/10.3390/ijms19103095 - 10 Oct 2018

Cited by 21 | Viewed by 3816

Abstract

Chloroplasts are the place for the major conversion of the sun’s radiation energy to chemical energy
that is usable by organisms[…] Full article

(This article belongs to the Special Issue Chloroplast)

Research

Jump to: Editorial, Review, Other

16 pages, 2173 KiB

Open AccessArticle

Nitric Oxide Enhancing Resistance to PEG-Induced Water Deficiency is Associated with the Primary Photosynthesis Reaction in Triticum aestivum L.

by Ruixin Shao, Huifang Zheng, Shuangjie Jia, Yanping Jiang, Qinghua Yang and Guozhang Kang

Int. J. Mol. Sci. 2018, 19(9), 2819; https://doi.org/10.3390/ijms19092819 - 18 Sep 2018

Cited by 13 | Viewed by 4515

Abstract

Photosynthesis is affected by water-deficiency (WD) stress, and nitric oxide (NO) is a free radical that participates in the photosynthesis process. Previous studies have suggested that NO regulates excitation-energy distribution of photosynthesis under WD stress. Here, quantitative phosphoproteomic profiling was conducted using iTRAQ. [...] Read more.

Photosynthesis is affected by water-deficiency (WD) stress, and nitric oxide (NO) is a free radical that participates in the photosynthesis process. Previous studies have suggested that NO regulates excitation-energy distribution of photosynthesis under WD stress. Here, quantitative phosphoproteomic profiling was conducted using iTRAQ. Differentially phosphorylated protein species (DEPs) were identified in leaves of NO- or polyethylene glycol (PEG)-treated wheat seedlings (D), and in control seedlings. From 1396 unique phosphoproteins, 2257 unique phosphorylated peptides and 2416 phosphorylation sites were identified. Of these, 96 DEPs displayed significant changes (≥1.50-fold, p < 0.01). These DEPs are involved in photosynthesis, signal transduction, etc. Furthermore, phosphorylation of several DEPs was upregulated by both D and NO treatments, but downregulated only in NO treatment. These differences affected the chlorophyll A–B binding protein, chloroplast post-illumination chlorophyll-fluorescence-increase protein, and SNT7, implying that NO indirectly regulated the absorption and transport of light energy in photosynthesis in response to WD stress. The significant difference of chlorophyll (Chl) content, Chl a fluorescence-transient, photosynthesis index, and trapping and transport of light energy further indicated that exogenous NO under D stress enhanced the primary photosynthesis reaction compared to D treatment. A putative pathway is proposed to elucidate NO regulation of the primary reaction of photosynthesis under WD. Full article

(This article belongs to the Special Issue Chloroplast)

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Figure 1

Figure 1
Change of relative water content (RWC) in leaves of wheat seedlings under normal water conditions and in response to three different treatments at different time points; a total of three independent biological replicates were conducted (n = 10). C, normal water conditions; S, pretreated with 150 µmol/L sodium nitroprusside; D, water deficiency induced by 20% polyethylene glycol (PEG)-6000; S + D, pretreated with 150 µmol/L sodium nitroprusside and water deficiency stress by 20% PEG-6000. Asterisks indicate significant differences among the four treatments at p < 0.05. Full article ">Figure 2
Phenotypic (A,B) changes in leaves of wheat seedlings under normal water conditions and in response to three different treatments; a total of three independent biological replicates were used (n = 10). For a detailed description of treatment conditions, please refer to the legend of <a href="#ijms-19-02819-f001" class="html-fig">Figure 1</a>. Different lowercase letters indicate a statistically significant difference at p < 0.05. Full article ">Figure 3
Upregulated and downregulated significant phosphorylated peptides among four groups. For a detailed description of treatment conditions, please refer to the legend of <a href="#ijms-19-02819-f001" class="html-fig">Figure 1</a>. Full article ">Figure 4
(A) Cluster analysis and (B) functional classification of significant differentially phosphorylated peptides in leaves of winter wheat among four different treatments. The color scale bar at the left of the hierarchical cluster analysis indicates the increased (red) and the decreased (green) peptides. For a detailed description of treatment conditions, please refer to the legend of <a href="#ijms-19-02819-f001" class="html-fig">Figure 1</a>. Full article ">Figure 5
(A) Chlorophyll (Chl) content (Chl a, Chl b), (B) net photosynthetic rate (Pn), (C) fluorescence intensity, PIABS, PET, and (D) RC/ABS in leaves of wheat seedlings under normal water conditions and in response to NO or PEG-induced water deficiency treatments. C, normal water conditions; S, pretreated with 150 µmol/L sodium nitroprusside; D, water deficiency induced by treatment with 20% polyethylene glycol (PEG)-6000; S + D, pretreated with 150 µmol/L sodium nitroprusside and then water deficiency stressed by 20% PEG-6000. O, J, I and P mean that the analysis of the transient-considered fluorescence values at 50 ms (Fo, step O), 2 ms (F2 ms, step J), 30 ms (F30 ms, step I), and maximal level (FM, step P), respectively. For a detailed description of treatment conditions, please refer to the legend of <a href="#ijms-19-02819-f001" class="html-fig">Figure 1</a>. Different lowercase letters in (A,B) indicate a statistically significant difference at p < 0.05. Full article ">Figure 6
Schematic representation of NO involved in the regulation of photosynthesis to improve water-deficiency stress resistance. The contribution of NO to photosynthesis primary reaction under water deficit stress flows in the direction indicated by the arrow. Full article ">

17 pages, 5580 KiB

Open AccessArticle

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus acutissima

by Xuan Li, Yongfu Li, Mingyue Zang, Mingzhi Li and Yanming Fang

Int. J. Mol. Sci. 2018, 19(8), 2443; https://doi.org/10.3390/ijms19082443 - 18 Aug 2018

Cited by 83 | Viewed by 8191

Abstract

Quercus acutissima, an important endemic and ecological plant of the Quercus genus, is widely distributed throughout China. However, there have been few studies on its chloroplast genome. In this study, the complete chloroplast (cp) genome of Q. acutissima was sequenced, analyzed, and [...] Read more.

Quercus acutissima, an important endemic and ecological plant of the Quercus genus, is widely distributed throughout China. However, there have been few studies on its chloroplast genome. In this study, the complete chloroplast (cp) genome of Q. acutissima was sequenced, analyzed, and compared to four species in the Fagaceae family. The size of the Q. acutissima chloroplast genome is 161,124 bp, including one large single copy (LSC) region of 90,423 bp and one small single copy (SSC) region of 19,068 bp, separated by two inverted repeat (IR) regions of 51,632 bp. The GC content of the whole genome is 36.08%, while those of LSC, SSC, and IR are 34.62%, 30.84%, and 42.78%, respectively. The Q. acutissima chloroplast genome encodes 136 genes, including 88 protein-coding genes, four ribosomal RNA genes, and 40 transfer RNA genes. In the repeat structure analysis, 31 forward and 22 inverted long repeats and 65 simple-sequence repeat loci were detected in the Q. acutissima cp genome. The existence of abundant simple-sequence repeat loci in the genome suggests the potential for future population genetic work. The genome comparison revealed that the LSC region is more divergent than the SSC and IR regions, and there is higher divergence in noncoding regions than in coding regions. The phylogenetic relationships of 25 species inferred that members of the Quercus genus do not form a clade and that Q. acutissima is closely related to Q. variabilis. This study identified the unique characteristics of the Q. acutissima cp genome, which will provide a theoretical basis for species identification and biological research. Full article

(This article belongs to the Special Issue Chloroplast)

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Graphical abstract

Graphical abstract
Full article ">Figure 1
Chloroplast genome map of Q. acutissima. Genes inside the circle are transcribed clockwise, and those outside are transcribed counterclockwise. Genes of different functions are color-coded. The darker gray in the inner circle shows the GC content, while the lighter gray shows the AT content. Full article ">Figure 2
Complete chloroplast genome comparison of six species using the chloroplast genome of Q. variabilis as a reference. The grey arrows and thick black lines above the alignment indicate the genes’ orientations. The Y-axis represents the identity from 50% to 100%. Full article ">Figure 3
Comparison of the large single copy (LSC), small single copy (SSC), and inverted repeat (IR) regions in chloroplast genomes of four species. Genes are denoted by colored boxes. The gaps between the genes and the boundaries are indicated by the base lengths (bp). Extensions of the genes are indicated above the boxes. Full article ">Figure 4
Bayesian inference (BI) phylogenetic tree reconstruction including 25 species based on all chloroplast genomes. Malus prunifolia and Ulmus gaussenii were used as the outgroup. Full article ">Figure A1
BLAST result of the chloroplast genome and the GC stew of Q. acutissima. BlAST 1 represents L. balansae; BlAST 2 represents Q. variabilis; BlAST 3 represents Q. dolicholepis. Full article ">Figure A2
Percentage of variation in the complete cp genomes of the six species. The regions are oriented according to their locations in the genome. Full article ">

16 pages, 6288 KiB

Open AccessArticle

Phylogenomic and Comparative Analyses of Complete Plastomes of Croomia and Stemona (Stemonaceae)

by Qixiang Lu, Wenqing Ye, Ruisen Lu, Wuqin Xu and Yingxiong Qiu

Int. J. Mol. Sci. 2018, 19(8), 2383; https://doi.org/10.3390/ijms19082383 - 13 Aug 2018

Cited by 30 | Viewed by 4501

Abstract

The monocot genus Croomia (Stemonaceae) comprises three herbaceous perennial species that exhibit EA (Eastern Asian)–ENA (Eastern North American) disjunct distribution. However, due to the lack of effective genomic resources, its evolutionary history is still weakly resolved. In the present study, we conducted comparative [...] Read more.

The monocot genus Croomia (Stemonaceae) comprises three herbaceous perennial species that exhibit EA (Eastern Asian)–ENA (Eastern North American) disjunct distribution. However, due to the lack of effective genomic resources, its evolutionary history is still weakly resolved. In the present study, we conducted comparative analysis of the complete chloroplast (cp) genomes of three Croomia species and two Stemona species. These five cp genomes proved highly similar in overall size (154,407–155,261 bp), structure, gene order and content. All five cp genomes contained the same 114 unique genes consisting of 80 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Gene content, gene order, AT content and IR/SC boundary structures were almost the same among the five Stemonaceae cp genomes, except that the Stemona cp genome was found to contain an inversion in cemA and petA. The lengths of five genomes varied due to contraction/expansion of the IR/SC borders. A/T mononucleotides were the richest Simple Sequence Repeats (SSRs). A total of 46, 48, 47, 61 and 60 repeats were identified in C. japonica, C. heterosepala, C. pauciflora, S. japonica and S. mairei, respectively. A comparison of pairwise sequence divergence values across all introns and intergenic spacers revealed that the ndhF–rpl32, psbM–trnD and trnS–trnG regions are the fastest-evolving regions. These regions are therefore likely to be the best choices for molecular evolutionary and systematic studies at low taxonomic levels in Stemonaceae. Phylogenetic analyses of the complete cp genomes and 78 protein-coding genes strongly supported the monophyly of Croomia. Two Asian species were identified as sisters that likely diverged in the Early Pleistocene (1.62 Mya, 95% HPD: 1.125–2.251 Mya), whereas the divergence of C. pauciflora dated back to the Late Miocene (4.77 Mya, 95% HPD: 3.626–6.162 Mya). The availability of these cp genomes will provide valuable genetic resources for further population genetics and phylogeographic studies on Croomia. Full article

(This article belongs to the Special Issue Chloroplast)

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15 pages, 12605 KiB

Open AccessArticle

Comparative Chloroplast Genome Analyses of Species in Gentiana section Cruciata (Gentianaceae) and the Development of Authentication Markers

by Tao Zhou, Jian Wang, Yun Jia, Wenli Li, Fusheng Xu and Xumei Wang

Int. J. Mol. Sci. 2018, 19(7), 1962; https://doi.org/10.3390/ijms19071962 - 5 Jul 2018

Cited by 67 | Viewed by 5294

Abstract

Gentiana section Cruciata is widely distributed across Eurasia at high altitudes, and some species in this section are used as traditional Chinese medicine. Accurate identification of these species is important for their utilization and conservation. Due to similar morphological and chemical characteristics, correct [...] Read more.

Gentiana section Cruciata is widely distributed across Eurasia at high altitudes, and some species in this section are used as traditional Chinese medicine. Accurate identification of these species is important for their utilization and conservation. Due to similar morphological and chemical characteristics, correct discrimination of these species still remains problematic. Here, we sequenced three complete chloroplast (cp) genomes (G. dahurica, G. siphonantha and G. officinalis). We further compared them with the previously published plastomes from sect. Cruciata and developed highly polymorphic molecular markers for species authentication. The eight cp genomes shared the highly conserved structure and contained 112 unique genes arranged in the same order, including 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. We analyzed the repeats and nucleotide substitutions in these plastomes and detected several highly variable regions. We found that four genes (accD, clpP, matK and ycf1) were subject to positive selection, and sixteen InDel-variable loci with high discriminatory powers were selected as candidate barcodes. Our phylogenetic analyses based on plastomes further confirmed the monophyly of sect. Cruciata and primarily elucidated the phylogeny of Gentianales. This study indicated that cp genomes can provide more integrated information for better elucidating the phylogenetic pattern and improving discriminatory power during species authentication. Full article

(This article belongs to the Special Issue Chloroplast)

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Graphical abstract

Graphical abstract
Full article ">Figure 1
Merged gene map of the complete chloroplast genomes of three Gentiana species. Genes belonging to different functional groups are classified by different colors. The genes drawn outside of the circle are transcribed counterclockwise, while those inside are clockwise. Dashed area in the inner circle represent GC content of chloroplast genome. Full article ">Figure 2
Comparison of chloroplast genome borders of LSC, SSC, and IRs among eight species in Gentiana sect. Cruciata. Ψ indicates a pseudogene. Full article ">Figure 3
Analysis of different repeats in eight chloroplast genomes of Gentiana sect. Cruciata. (A) Histogram showing the number of palindromic repeats and dispersed repeats; (B) histogram showing the number of tandem repeats; (C) number of different simple sequence repeat (SSR) types detected in eight chloroplast genomes; (D) total numbers of different SSR motifs in eight chloroplast genomes. Full article ">Figure 4
mVISTA percent identity plot comparing the eight chloroplast genomes of Gentiana sect. Cruciata with G. crassicaulis as a reference. The y-axis represents the percent identity within 50–100%. Genome regions are color-coded as protein coding (purple), rRNA, or tRNA coding genes (blue), and noncoding sequences (pink). Full article ">Figure 5
Percentage of variable characters in eight aligned chloroplast genomes of Gentiana sect. Cruciata. (A) Coding region; (B) Noncoding region. Full article ">Figure 6
Validation of 16 molecular markers derived from InDel regions of eight chloroplast genomes of Gentiana sect. Cruciata. Inserted sequences and tandem repeats are designated by diamonds and triangle, respectively. Solid and dotted lines indicate conserved and deleted sequences, respectively. Left and right black arrows indicate forward and reverse primers, respectively. Abbreviated species names were shown on schematic diagrams: Gd, G. dahurica; Go, G. officinalis; Gm, G. macrophylla; Gsi, G. siphonantha; Gst, G. straminea; Gr, G. robusta; Gc, G. crassicaulis; M, D600 DNA ladder. Full article ">Figure 7
Phylogenetic relationships of species belong to Gentiana sect. Cruciata inferred from MP/ML/BI analysis based on complete chloroplast genome sequences. The numbers associated with each node are bootstrap support and posterior probability values, and the symbol <img alt="Ijms 19 01962 i001" src="/ijms/ijms-19-01962/article_deploy/html/images/ijms-19-01962-i001.png"/> in the phylogenetic tree indicated that the support value of branch is 100/100/1.0. Full article ">

20 pages, 4877 KiB

Open AccessArticle

Comparative Analysis of the Chloroplast Genomes of the Chinese Endemic Genus Urophysa and Their Contribution to Chloroplast Phylogeny and Adaptive Evolution

by Deng-Feng Xie, Yan Yu, Yi-Qi Deng, Juan Li, Hai-Ying Liu, Song-Dong Zhou and Xing-Jin He

Int. J. Mol. Sci. 2018, 19(7), 1847; https://doi.org/10.3390/ijms19071847 - 22 Jun 2018

Cited by 81 | Viewed by 5638

Abstract

Urophysa is a Chinese endemic genus comprising two species, Urophysa rockii and Urophysa henryi. In this study, we sequenced the complete chloroplast (cp) genomes of these two species and of their relative Semiquilegia adoxoides. Illumina sequencing technology was used to compare [...] Read more.

Urophysa is a Chinese endemic genus comprising two species, Urophysa rockii and Urophysa henryi. In this study, we sequenced the complete chloroplast (cp) genomes of these two species and of their relative Semiquilegia adoxoides. Illumina sequencing technology was used to compare sequences, elucidate the intra- and interspecies variations, and infer the phylogeny relationship with other Ranunculaceae family species. A typical quadripartite structure was detected, with a genome size from 158,473 to 158,512 bp, consisting of a pair of inverted repeats separated by a small single-copy region and a large single-copy region. We analyzed the nucleotide diversity and repeated sequences components and conducted a positive selection analysis by the codon-based substitution on single-copy coding sequence (CDS). Seven regions were found to possess relatively high nucleotide diversity, and numerous variable repeats and simple sequence repeats (SSR) markers were detected. Six single-copy genes (atpA, rpl20, psaA, atpB, ndhI, and rbcL) resulted to have high posterior probabilities of codon sites in the positive selection analysis, which means that the six genes may be under a great selection pressure. The visualization results of the six genes showed that the amino acid properties across each column of all species are variable in different genera. All these regions with high nucleotide diversity, abundant repeats, and under positive selection will provide potential plastid markers for further taxonomic, phylogenetic, and population genetics studies in Urophysa and its relatives. Phylogenetic analyses based on the 79 single-copy genes, the whole complete genome sequences, and all CDS sequences showed same topologies with high support, and U. rockii was closely clustered with U. henryi within the Urophysa genus, with S. adoxoides as their closest relative. Therefore, the complete cp genomes in Urophysa species provide interesting insights and valuable information that can be used to identify related species and reconstruct their phylogeny. Full article

(This article belongs to the Special Issue Chloroplast)

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Figure 1
Gene maps of the Urophysa rockii, Urophysa henryi and Semiquilegia adoxoides chloroplast (cp) genomes. Genes shown inside the circle are transcribed clockwise, and those outside are transcribed counterclockwise. Genes belonging to different functional groups are color-coded. The darker gray color in the inner circle corresponds to the GC content, and the lighter gray color corresponds to the AT content. SSU: small subunit; LSU: large subunit; ORF: open reading frame. Full article ">Figure 2
Analysis of repeated sequences in U. rockii, U. henryi, and S. adoxoides chloroplast genomes. (A) Total of four repeat types; (B) Frequency of the palindromic repeat by length; (C) Frequency of the forward repeat by length; (D) Frequency of the reverse repeat by length. Full article ">Figure 3
Analysis of simple sequence repeats (SSRs) in chloroplast genomes of the three species. (A) Number of different SSR types detected in each species; (B) type and frequency of each identified SSR. Full article ">Figure 4
The nucleotide diversity of the whole chloroplast genomes of the three species. LSC: large single-copy region; IRs: inverted repeats region; SSC: small single-copy region. Full article ">Figure 5
Comparison of the borders of the LSC, SSC, and IR regions of the chloroplast genomes of the three species. LR: junction line between LSC and IRb; RS: junction line between IRb and SSC; SR: junction line between SSC and IRa; RL: junction line between IRa and LSC. Full article ">Figure 6
Phylogenetic relationship of Urophysa with related species based on 79 single-copy genes shared by all cp genomes. Tree constructed by (A) maximum likelihood (ML) with the bootstrap values of ML above the branches; (B) maximum parsimony (MP) and Bayesian inference (BI) with bootstrap values of MP and posterior probabilities of BI above the branches, respectively. Full article ">Figure 7
Two of the amino acids sequences that showed positive selection in the branch-site model test. (A) Amino acids sequences of the rpl20 gene; (B) amino acids sequences of the ndhI gene. The red blocks represent the different amino acids. Full article ">

26 pages, 4657 KiB

Open AccessArticle

Candidate Genes for Yellow Leaf Color in Common Wheat (Triticum aestivum L.) and Major Related Metabolic Pathways according to Transcriptome Profiling

by Huiyu Wu, Narong Shi, Xuyao An, Cong Liu, Hongfei Fu, Li Cao, Yi Feng, Daojie Sun and Lingli Zhang

Int. J. Mol. Sci. 2018, 19(6), 1594; https://doi.org/10.3390/ijms19061594 - 29 May 2018

Cited by 70 | Viewed by 6989

Abstract

The photosynthetic capacity and efficiency of a crop depends on the biosynthesis of photosynthetic pigments and chloroplast development. However, little is known about the molecular mechanisms of chloroplast development and chlorophyll (Chl) biosynthesis in common wheat because of its huge and complex genome. [...] Read more.

The photosynthetic capacity and efficiency of a crop depends on the biosynthesis of photosynthetic pigments and chloroplast development. However, little is known about the molecular mechanisms of chloroplast development and chlorophyll (Chl) biosynthesis in common wheat because of its huge and complex genome. Ygm, a spontaneous yellow-green leaf color mutant of winter wheat, exhibits reduced Chl contents and abnormal chloroplast development. Thus, we searched for candidate genes associated with this phenotype. Comparative transcriptome profiling was performed using leaves from the yellow leaf color type (Y) and normal green color type (G) of the Ygm mutant progeny. We identified 1227 differentially expressed genes (DEGs) in Y compared with G (i.e., 689 upregulated genes and 538 downregulated genes). Gene ontology and pathway enrichment analyses indicated that the DEGs were involved in Chl biosynthesis (i.e., magnesium chelatase subunit H (CHLH) and protochlorophyllide oxidoreductase (POR) genes), carotenoid biosynthesis (i.e., β-carotene hydroxylase (BCH) genes), photosynthesis, and carbon fixation in photosynthetic organisms. We also identified heat shock protein (HSP) genes (sHSP, HSP70, HSP90, and DnaJ) and heat shock transcription factor genes that might have vital roles in chloroplast development. Quantitative RT-PCR analysis of the relevant DEGs confirmed the RNA-Seq results. Moreover, measurements of seven intermediate products involved in Chl biosynthesis and five carotenoid compounds involved in carotenoid-xanthophyll biosynthesis confirmed that CHLH and BCH are vital enzymes for the unusual leaf color phenotype in Y type. These results provide insights into leaf color variation in wheat at the transcriptional level. Full article

(This article belongs to the Special Issue Chloroplast)

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17 pages, 2782 KiB

Open AccessArticle

Sequencing, Characterization, and Comparative Analyses of the Plastome of Caragana rosea var. rosea

by Mei Jiang, Haimei Chen, Shuaibing He, Liqiang Wang, Amanda Juan Chen and Chang Liu

Int. J. Mol. Sci. 2018, 19(5), 1419; https://doi.org/10.3390/ijms19051419 - 9 May 2018

Cited by 33 | Viewed by 4561

Abstract

To exploit the drought-resistant Caragana species, we performed a comparative study of the plastomes from four species: Caragana rosea, C. microphylla, C. kozlowii, and C. Korshinskii. The complete plastome sequence of the C. rosea was obtained using the next [...] Read more.

To exploit the drought-resistant Caragana species, we performed a comparative study of the plastomes from four species: Caragana rosea, C. microphylla, C. kozlowii, and C. Korshinskii. The complete plastome sequence of the C. rosea was obtained using the next generation DNA sequencing technology. The genome is a circular structure of 133,122 bases and it lacks inverted repeat. It contains 111 unique genes, including 76 protein-coding, 30 tRNA, and four rRNA genes. Repeat analyses obtained 239, 244, 258, and 246 simple sequence repeats in C. rosea, C. microphylla, C. kozlowii, and C. korshinskii, respectively. Analyses of sequence divergence found two intergenic regions: trnI-CAU-ycf2 and trnN-GUU-ycf1, exhibiting a high degree of variations. Phylogenetic analyses showed that the four Caragana species belong to a monophyletic clade. Analyses of Ka/Ks ratios revealed that five genes: rpl16, rpl20, rps11, rps7, and ycf1 and several sites having undergone strong positive selection in the Caragana branch. The results lay the foundation for the development of molecular markers and the understanding of the evolutionary process for drought-resistant characteristics. Full article

(This article belongs to the Special Issue Chloroplast)

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Figure 1

Figure 1
Circular gene map of the C. rosea plastome. Genes drawn inside the circle are transcribed clockwise, and those outside the circle are transcribed counterclockwise. Genes belonging to different functional groups are color codes. The inner circle shows the GC content. The two grey arrows represent the direction of transcription. Full article ">Figure 2
Statistics of simple sequence repeat (SSRs) detected in the plastome of four Caragana species. (A) Numbers of SSRs found in the coding (CDS), intergenic (IGS), and intronic regions, respectively; (B) number of different SSR types identified in the four genomes; and, (C) number of identified SSR motifs in different repeat class types. Full article ">Figure 3
Structure comparison of the four plastomes by using the mVISTA program. Gray arrows and thick black lines above the alignment indicate genes with their orientation and the position of the IRs, respectively. A cut-off value of 70% identity was used for the plots, and the Y-scale represents the percent identity between 50% and 100%. UTR: Untranlated Regions; CNS: Conserved Non-coding Sequences. A: IGS(rps12-clpP); B: IGS(rps19-rp12); C: IGS(psaC-ndhD). Full article ">Figure 4
K2p distances for introns among C. rosea, C. microphylla, C. kozlowii, and C. korshinskii. Full article ">Figure 5
K2p distances for IGS regions among C. rosea, C. microphylla, C. kozlowii, and C. korshinskii. Full article ">Figure 6
Molecular phylogenetic analyses of plastomes in the inverted-repeat-lacking clade of Papilionoideae. The tree was constructed with the sequences of 63 proteins present in all 36 species by using the maximum likelihood method implemented in RAxML. Bootstrap supports were calculated from 1000 replicates. Nicotiana tabacum and Arabidopsis thaliana were set as outgroups. Full article ">

17 pages, 4502 KiB

Open AccessArticle

Complete Chloroplast Genome of Cercis chuniana (Fabaceae) with Structural and Genetic Comparison to Six Species in Caesalpinioideae

by Wanzhen Liu, Hanghui Kong, Juan Zhou, Peter W. Fritsch, Gang Hao and Wei Gong

Int. J. Mol. Sci. 2018, 19(5), 1286; https://doi.org/10.3390/ijms19051286 - 25 Apr 2018

Cited by 35 | Viewed by 5485

Abstract

The subfamily Caesalpinioideae of the Fabaceae has long been recognized as non-monophyletic due to its controversial phylogenetic relationships. Cercis chuniana, endemic to China, is a representative species of Cercis L. placed within Caesalpinioideae in the older sense. Here, we report the whole [...] Read more.

The subfamily Caesalpinioideae of the Fabaceae has long been recognized as non-monophyletic due to its controversial phylogenetic relationships. Cercis chuniana, endemic to China, is a representative species of Cercis L. placed within Caesalpinioideae in the older sense. Here, we report the whole chloroplast (cp) genome of C. chuniana and compare it to six other species from the Caesalpinioideae. Comparative analyses of gene synteny and simple sequence repeats (SSRs), as well as estimation of nucleotide diversity, the relative ratios of synonymous and nonsynonymous substitutions (dn/ds), and Kimura 2-parameter (K2P) interspecific genetic distances, were all conducted. The whole cp genome of C. chuniana was found to be 158,433 bp long with a total of 114 genes, 81 of which code for proteins. Nucleotide substitutions and length variation are present, particularly at the boundaries among large single copy (LSC), inverted repeat (IR) and small single copy (SSC) regions. Nucleotide diversity among all species was estimated to be 0.03, the average dn/ds ratio 0.3177, and the average K2P value 0.0372. Ninety-one SSRs were identified in C. chuniana, with the highest proportion in the LSC region. Ninety-seven species from the old Caesalpinioideae were selected for phylogenetic reconstruction, the analysis of which strongly supports the monophyly of Cercidoideae based on the new classification of the Fabaceae. Our study provides genomic information for further phylogenetic reconstruction and biogeographic inference of Cercis and other legume species. Full article

(This article belongs to the Special Issue Chloroplast)

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Graphical abstract
Full article ">Figure 1
Gene map of the Cercis chuniana cp genome. The genes lying inside and outside the outer circle are transcribed in clockwise and counterclockwise direction, respectively (as indicated by arrows). Colors denote the genes belonging to different functional groups. The hatch marks on the inner circle indicate the extent of the inverted repeats (IRa and IRb) that separate the small single copy (SSC) region from the large single copy (LSC) region. The dark gray and light gray shading within the inner circle correspond to percentage G + C and A + T content, respectively. Full article ">Figure 2
Comparison of the border positions of LSC, SSC and IR regions among the seven species of caesalpinioid legumes compared in this study. Genes are denoted by colored boxes. The gaps between the genes and the boundaries are indicated by the base lengths (bp). Extensions of the genes are indicated above the boxes. Full article ">Figure 3
Analysis of repeated sequences of the seven species compared in this study. (a) The number of SSRs distributed in different regions; (b) The number of SSRs with different types, including compound, mono-, di-, tri-, and tetranucleotides; (c) The proportion of SSRs with different lengths. Full article ">Figure 4
Sliding window analysis of the whole cp genome. (a) C. chuniana and C. canadensis; (b) All seven species. X-axis: position of the midpoint of a window; Y-axis: nucleotide diversity (π) of each window. Full article ">Figure 5
Evolutionary dynamics of genes in the cp genomes. (a) The dn/ds ratios for individual genes; (b) The K2P values for individual genes. Full article ">Figure 6
Phylogenetic trees of sampled species inferred from the concatenated whole cp genome sequences and 61 protein-coding genes (PCGs) in the cp genome based on maximum likelihood (ML) and Bayesian inference (BI). (a) ML analysis based on whole cp genome sequences; (b) BI analysis based on whole cp genome sequences; (c) ML analysis based on PCGs; (d) BI analysis based on PCGs. Numbers in bold above branches are bootstrap values ≥50% and Bayesian posterior probability values ≥90%. Full article ">

16 pages, 6591 KiB

Open AccessArticle

Comparative Plastid Genomes of Primula Species: Sequence Divergence and Phylogenetic Relationships

by Ting Ren, Yanci Yang, Tao Zhou and Zhan-Lin Liu

Int. J. Mol. Sci. 2018, 19(4), 1050; https://doi.org/10.3390/ijms19041050 - 1 Apr 2018

Cited by 47 | Viewed by 5724

Abstract

Compared to traditional DNA markers, genome-scale datasets can provide mass information to effectively address historically difficult phylogenies. Primula is the largest genus in the family Primulaceae, with members distributed mainly throughout temperate and arctic areas of the Northern Hemisphere. The phylogenetic relationships among [...] Read more.

Compared to traditional DNA markers, genome-scale datasets can provide mass information to effectively address historically difficult phylogenies. Primula is the largest genus in the family Primulaceae, with members distributed mainly throughout temperate and arctic areas of the Northern Hemisphere. The phylogenetic relationships among Primula taxa still maintain unresolved, mainly due to intra- and interspecific morphological variation, which was caused by frequent hybridization and introgression. In this study, we sequenced and assembled four complete plastid genomes (Primula handeliana, Primula woodwardii, Primula knuthiana, and Androsace laxa) by Illumina paired-end sequencing. A total of 10 Primula species (including 7 published plastid genomes) were analyzed to investigate the plastid genome sequence divergence and their inferences for the phylogeny of Primula. The 10 Primula plastid genomes were similar in terms of their gene content and order, GC content, and codon usage, but slightly different in the number of the repeat. Moderate sequence divergence was observed among Primula plastid genomes. Phylogenetic analysis strongly supported that Primula was monophyletic and more closely related to Androsace in the Primulaceae family. The phylogenetic relationships among the 10 Primula species showed that the placement of P. knuthiana–P. veris clade was uncertain in the phylogenetic tree. This study indicated that plastid genome data were highly effective to investigate the phylogeny. Full article

(This article belongs to the Special Issue Chloroplast)

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Graphical abstract

Graphical abstract
Full article ">Figure 1
The type of repeated sequences in the 10 Primula plastid genomes. (A) Number of three repeat types; (B) number of repeat sequences by length. Full article ">Figure 2
Simple sequence repeats (SSRs) in the 10 Primula plastid genomes. (A) Number of SSR types; (B) number of mononucleotide A/T and G/C SSRs. Full article ">Figure 3
Comparison of the LSC, IR, and SSC border regions among the 10 Primula plastid genomes. Number above the gene features means the distance between the ends of genes and the borders sites. These features are not to scale. Full article ">Figure 4
Sequence identity plot of the 10 Primula plastid genomes, with Primula poissonii as a reference. The y-axis represents % identity ranging from 50% to 100%. Coding and non-coding regions are marked in purple and pink, respectively. The red, black, and gray lines show the IRs, LSC, and SSC regions, respectively. Full article ">Figure 5
Phylogenetic relationship of the 31 species inferred from ML and BI analyses based on 76 shared protein-coding genes. The numbers near each node are bootstrap support values and posterior probability. Hydrangea petiolaris and Hydrangea serrata were used as the outgroups. Full article ">Figure 6
Phylogenetic relationships of the 10 Primula species and A. laxa inferred from ML and BI analyses. (A) Whole plastid genomes; (B) protein-coding regions; (C) introns and intergenic spacer regions; (D) IR regions; (E) SSC regions; and (F) LSC regions. The numbers near each node are bootstrap support values and posterior probability. Full article ">

15 pages, 22427 KiB

Open AccessArticle

Different Natural Selection Pressures on the atpF Gene in Evergreen Sclerophyllous and Deciduous Oak Species: Evidence from Comparative Analysis of the Complete Chloroplast Genome of Quercus aquifolioides with Other Oak Species

by Kangquan Yin, Yue Zhang, Yuejuan Li and Fang K. Du

Int. J. Mol. Sci. 2018, 19(4), 1042; https://doi.org/10.3390/ijms19041042 - 30 Mar 2018

Cited by 41 | Viewed by 5763

Abstract

Quercus is an economically important and phylogenetically complex genus in the family Fagaceae. Due to extensive hybridization and introgression, it is considered to be one of the most challenging plant taxa, both taxonomically and phylogenetically. Quercus aquifolioides is an evergreen sclerophyllous oak species [...] Read more.

Quercus is an economically important and phylogenetically complex genus in the family Fagaceae. Due to extensive hybridization and introgression, it is considered to be one of the most challenging plant taxa, both taxonomically and phylogenetically. Quercus aquifolioides is an evergreen sclerophyllous oak species that is endemic to, but widely distributed across, the Hengduanshan Biodiversity Hotspot in the Eastern Himalayas. Here, we compared the fully assembled chloroplast (cp) genome of Q. aquifolioides with those of three closely related species. The analysis revealed a cp genome ranging in size from 160,415 to 161,304 bp and with a typical quadripartite structure, composed of two inverted repeats (IRs) separated by a small single copy (SSC) and a large single copy (LSC) region. The genome organization, gene number, gene order, and GC content of these four Quercus cp genomes are similar to those of many angiosperm cp genomes. We also analyzed the Q. aquifolioides repeats and microsatellites. Investigating the effects of selection events on shared protein-coding genes using the Ka/Ks ratio showed that significant positive selection had acted on the atpF gene of Q. aquifolioides compared to two deciduous oak species, and that there had been significant purifying selection on the atpF gene in the chloroplast of evergreen sclerophyllous oak trees. In addition, site-specific selection analysis identified positively selected sites in 12 genes. Phylogenetic analysis based on shared protein-coding genes from 14 species defined Q. aquifolioides as belonging to sect. Heterobalanus and being closely related to Q. rubra and Q. aliena. Our findings provide valuable genetic information for use in accurately identifying species, resolving taxonomy, and reconstructing the phylogeny of the genus Quercus. Full article

(This article belongs to the Special Issue Chloroplast)

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16 pages, 4201 KiB

Open AccessArticle

Whole-Genome Comparison Reveals Heterogeneous Divergence and Mutation Hotspots in Chloroplast Genome of Eucommia ulmoides Oliver

by Wencai Wang, Siyun Chen and Xianzhi Zhang

Int. J. Mol. Sci. 2018, 19(4), 1037; https://doi.org/10.3390/ijms19041037 - 30 Mar 2018

Cited by 30 | Viewed by 5173

Abstract

Eucommia ulmoides (E. ulmoides), the sole species of Eucommiaceae with high importance of medicinal and industrial values, is a Tertiary relic plant that is endemic to China. However, the population genetics study of E. ulmoides lags far behind largely due to [...] Read more.

Eucommia ulmoides (E. ulmoides), the sole species of Eucommiaceae with high importance of medicinal and industrial values, is a Tertiary relic plant that is endemic to China. However, the population genetics study of E. ulmoides lags far behind largely due to the scarcity of genomic data. In this study, one complete chloroplast (cp) genome of E. ulmoides was generated via the genome skimming approach and compared to another available E. ulmoides cp genome comprehensively at the genome scale. We found that the structure of the cp genome in E. ulmoides was highly consistent with genome size variation which might result from DNA repeat variations in the two E. ulmoides cp genomes. Heterogeneous sequence divergence patterns were revealed in different regions of the E. ulmoides cp genomes, with most (59 out of 75) of the detected SNPs (single nucleotide polymorphisms) located in the gene regions, whereas most (50 out of 80) of the indels (insertions/deletions) were distributed in the intergenic spacers. In addition, we also found that all the 40 putative coding-region-located SNPs were synonymous mutations. A total of 71 polymorphic cpDNA fragments were further identified, among which 20 loci were selected as potential molecular markers for subsequent population genetics studies of E. ulmoides. Moreover, eight polymorphic cpSSR loci were also developed. The sister relationship between E. ulmoides and Aucuba japonica in Garryales was also confirmed based on the cp phylogenomic analyses. Overall, this study will shed new light on the conservation genomics of this endangered plant in the future. Full article

(This article belongs to the Special Issue Chloroplast)

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Graphical abstract

Graphical abstract
Full article ">Figure 1
Conserved chloroplast genome structure in Eucommia ulmoides. (A) Pairwise chloroplast genome alignments derived from Multiple Alignment using Fast Fourier Transform (MAFFT) program. The sequence identity is indicated on the top. Label KU204775.1 represents the E. ulmoides chloroplast genome retrieved from GenBank, while label E. ulmoides indicates the newly sequenced genome in this study. (B) Pairwise chloroplast genome alignments derived from MAUVE software. Full article ">Figure 2
Mutational events (SNPs and indels) detected across the chloroplast genome of Eucommia ulmoides. SNPs (single nucleotide polymorphisms) indicate nucleotide substitutions and indels represent nucleotide insertions and deletions. The homologous loci are oriented according to their locations in the chloroplast genome. Full article ">Figure 3
Percentage of variable characters (SNPs and indels) in polymorphic chloroplast loci in Eucommia ulmoides. The homologous loci are oriented according to their locations in the chloroplast genome. Full article ">Figure 4
Maximum likelihood (ML) tree for 34 taxa based on 80 unique plastid protein-coding genes of Eucommia ulmoides. Values above the branches represent maximum parsimony bootstrap (MPBS)/maximum likelihood bootstrap (MLBS)/Bayesian inference posterior probability (PP). The newly sequenced Eucommia ulmoides chloroplast genome is indicated by red color and the previously published E. ulmoides chloroplast genome is followed by its GenBank accession number KU204775. Full article ">

18 pages, 3442 KiB

Open AccessArticle

The Complete Chloroplast Genome Sequence of Tree of Heaven (Ailanthus altissima (Mill.) (Sapindales: Simaroubaceae), an Important Pantropical Tree

by Josphat K. Saina, Zhi-Zhong Li, Andrew W. Gichira and Yi-Ying Liao

Int. J. Mol. Sci. 2018, 19(4), 929; https://doi.org/10.3390/ijms19040929 - 21 Mar 2018

Cited by 68 | Viewed by 6240

Abstract

Ailanthus altissima (Mill.) Swingle (Simaroubaceae) is a deciduous tree widely distributed throughout temperate regions in China, hence suitable for genetic diversity and evolutionary studies. Previous studies in A. altissima have mainly focused on its biological activities, genetic diversity and genetic structure. However, until [...] Read more.

Ailanthus altissima (Mill.) Swingle (Simaroubaceae) is a deciduous tree widely distributed throughout temperate regions in China, hence suitable for genetic diversity and evolutionary studies. Previous studies in A. altissima have mainly focused on its biological activities, genetic diversity and genetic structure. However, until now there is no published report regarding genome of this plant species or Simaroubaceae family. Therefore, in this paper, we first characterized A. altissima complete chloroplast genome sequence. The tree of heaven chloroplast genome was found to be a circular molecule 160,815 base pairs (bp) in size and possess a quadripartite structure. The A. altissima chloroplast genome contains 113 unique genes of which 79 and 30 are protein coding and transfer RNA (tRNA) genes respectively and also 4 ribosomal RNA genes (rRNA) with overall GC content of 37.6%. Microsatellite marker detection identified A/T mononucleotides as majority SSRs in all the seven analyzed genomes. Repeat analyses of seven Sapindales revealed a total of 49 repeats in A. altissima, Rhus chinensis, Dodonaea viscosa, Leitneria floridana, while Azadirachta indica, Boswellia sacra, and Citrus aurantiifolia had a total of 48 repeats. The phylogenetic analysis using protein coding genes revealed that A. altissima is a sister to Leitneria floridana and also suggested that Simaroubaceae is a sister to Rutaceae family. The genome information reported here could be further applied for evolution and invasion, population genetics, and molecular studies in this plant species and family. Full article

(This article belongs to the Special Issue Chloroplast)

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Figure 1

Figure 1
Circular gene map of A. altissima complete chloroplast genome. Genes drawn on the outside of the circle are transcribed clockwise, whereas those inside are transcribed clockwise. The light gray in the inner circle corresponds to AT content, while the darker gray corresponds to the GC content. Large single copy (LSC), Inverted repeats (IRa and IRb), and Small single copy (SSC) are indicated. Full article ">Figure 2
Comparison of IR, LSC and SSC junction positions among seven Chloroplast genomes. The features drawn are not to scale. The symbol ᵠ means pseudogene created by IRb/SSC border extension into ycf1 genes. Colored boxes for genes represent the gene position. Full article ">Figure 3
Gene arrangement map of seven chloroplast genomes representing families from Sapindales, and one reference species (Aquilaria sinensis) aligned using Mauve software Local collinear blocks within each alignment are represented in as blocks of similar color connected with lines. Annotations of rRNA, protein coding and tRNA genes are shown in red, white and green boxes respectively. Full article ">Figure 4
Amino acid frequencies in A. altissima chloroplast genome protein coding sequences. Full article ">Figure 5
Simple sequence repeat (SSRs) type, distribution and presence in A. altissima and other representative species from Sapindales. (A) Number of detected SSR motifs in different repeat types in A. altissima Chloroplast genome. (B) Number of identified repeat sequences in seven chloroplast genomes. (C) Number of different SSR types in seven representative species. F, indicate (forward), P (palindromic), R (reverse), and C (complement), while P1, P2, P3, P4, P5 indicates Mono-, di-, tri-, tetra-, and penta-nucleotides respectively. F: forward; P: palindromic, R: reverse; C: complement. Full article ">Figure 6
Phylogenetic tree of 31 Sapindales species with three outgroup Malvales species inferred from ML (Maximum likelihood) based on common protein coding genes. The position of A. altissima is shown in bold, while bootstrap support values are shown at each node. Full article ">

20 pages, 7120 KiB

Open AccessArticle

Molecular Evolution of Chloroplast Genomes of Orchid Species: Insights into Phylogenetic Relationship and Adaptive Evolution

by Wan-Lin Dong, Ruo-Nan Wang, Na-Yao Zhang, Wei-Bing Fan, Min-Feng Fang and Zhong-Hu Li

Int. J. Mol. Sci. 2018, 19(3), 716; https://doi.org/10.3390/ijms19030716 - 2 Mar 2018

Cited by 130 | Viewed by 8113

Abstract

Orchidaceae is the 3rd largest family of angiosperms, an evolved young branch of monocotyledons. This family contains a number of economically-important horticulture and flowering plants. However, the limited availability of genomic information largely hindered the study of molecular evolution and phylogeny of Orchidaceae. [...] Read more.

Orchidaceae is the 3rd largest family of angiosperms, an evolved young branch of monocotyledons. This family contains a number of economically-important horticulture and flowering plants. However, the limited availability of genomic information largely hindered the study of molecular evolution and phylogeny of Orchidaceae. In this study, we determined the evolutionary characteristics of whole chloroplast (cp) genomes and the phylogenetic relationships of the family Orchidaceae. We firstly characterized the cp genomes of four orchid species: Cremastra appendiculata, Calanthe davidii, Epipactis mairei, and Platanthera japonica. The size of the chloroplast genome ranged from 153,629 bp (C. davidi) to 160,427 bp (E. mairei). The gene order, GC content, and gene compositions are similar to those of other previously-reported angiosperms. We identified that the genes of ndhC, ndhI, and ndhK were lost in C. appendiculata, in that the ndh I gene was lost in P. japonica and E. mairei. In addition, the four types of repeats (forward, palindromic, reverse, and complement repeats) were examined in orchid species. E. mairei had the highest number of repeats (81), while C. davidii had the lowest number (57). The total number of Simple Sequence Repeats is at least 50 in C. davidii, and, at most, 78 in P. japonica. Interestingly, we identified 16 genes with positive selection sites (the psbH, petD, petL, rpl22, rpl32, rpoC1, rpoC2, rps12, rps15, rps16, accD, ccsA, rbcL, ycf1, ycf2, and ycf4 genes), which might play an important role in the orchid species’ adaptation to diverse environments. Additionally, 11 mutational hotspot regions were determined, including five non-coding regions (ndhB intron, ccsA-ndhD, rpl33-rps18, ndhE-ndhG, and ndhF-rpl32) and six coding regions (rps16, ndhC, rpl32, ndhI, ndhK, and ndhF). The phylogenetic analysis based on whole cp genomes showed that C. appendiculata was closely related to C. striata var. vreelandii, while C. davidii and C. triplicate formed a small monophyletic evolutionary clade with a high bootstrap support. In addition, five subfamilies of Orchidaceae, Apostasioideae, Cypripedioideae, Epidendroideae, Orchidoideae, and Vanilloideae, formed a nested evolutionary relationship in the phylogenetic tree. These results provide important insights into the adaptive evolution and phylogeny of Orchidaceae. Full article

(This article belongs to the Special Issue Chloroplast)

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Figure 1

Figure 1
Chloroplast genome maps of the four orchid species. Gene locations outside of the outer rim are transcribed in the counter clockwise direction, whereas genes inside are transcribed in the clockwise direction. The colored bars indicate known different functional groups. The dashed gray area in the inner circle shows the proportional GC content of the corresponding genes. LSC, SSC and IR are large single-copy region, small single-copy region, and inverted repeat region, respectively. Full article ">Figure 2
Maps of repeat sequence analyses. Repeat sequences in C. appendiculata, C. davidii, E. mairei, and P. japonica chloroplast genomes. (a) Number of the four repeat types, F, P, R, and C, indicate the repeat type (F: forward, P: palindrome, R: reverse, and C: complement, respectively). (b) Frequency of the four repeat types by length. (c) Repeat distribution among four different regions: IGS: intergenic spacer, CDS: coding sequence, intron and CDS-IGS part in CDS and part in IGS. Full article ">Figure 3
The distribution maps of simple sequence repeats (SSR) in C. appendiculata, C. davidii, E. mairei, and P. japonica chloroplast genomes. (a) Classification of SSRs in four orchid species. IGS, intergenic spacer; CDS, coding sequence, CDS-IGS, part in CDS and part in IGS. (b) Classification of SSRs by repeat type. mono-, mononucleotides; di-, dinucleotides; tri-, trinucleotides; tetra-, tetranucleotides; penta-, pentanucleotides; and hexa-, hexanucleotides. Full article ">Figure 4
Comparison of the borders of LSC, SSC, and IR regions in 20 orchid complete chloroplast genomes. Full article ">Figure 5
Sequence alignment of chloroplast genomes of 20 orchid species. Sequence identity plot comparing the chloroplast genomes with C. appendiculata as a reference using mVISTA. The red color-coded as intergenic spacer regions. The blue color-coded as gene regions. A cut-off of 70% identity was used for the plots, and the Y-scale represents the percent identity between 50% and 100%. Full article ">Figure 6
Percentages of variable sites in homologous regions across the 20 orchids with complete chloroplast genomes. (a) The introns and spacers (IGS); and (b) protein coding sequences (CDS). Full article ">Figure 7
MAUVE genome alignments of the 20 orchid chloroplast genomes, with C. appendiculata set as a reference genome. The corresponding colored boxes indicate locally-collinear blocks, which present homologous gene clusters. The red vertical line is the location of atpH gene. The yellow vertical line is the location of petN gene. The green vertical line is the location of psbM gene. The blue vertical line is the location of ycf2 gene. Full article ">Figure 8
Cladogram of 54 nucleotide sequences of complete chloroplast genomes of orchid species based on the GTRGAMMA model with maximum likelihood (ML) analysis. * The newly generated chloroplast genomes of orchid species. Full article ">

15 pages, 2490 KiB

Open AccessArticle

The Complete Plastome Sequence of an Antarctic Bryophyte Sanionia uncinata (Hedw.) Loeske

by Mira Park, Hyun Park, Hyoungseok Lee, Byeong-ha Lee and Jungeun Lee

Int. J. Mol. Sci. 2018, 19(3), 709; https://doi.org/10.3390/ijms19030709 - 1 Mar 2018

Cited by 38 | Viewed by 5292

Abstract

Organellar genomes of bryophytes are poorly represented with chloroplast genomes of only four mosses, four liverworts and two hornworts having been sequenced and annotated. Moreover, while Antarctic vegetation is dominated by the bryophytes, there are few reports on the plastid genomes for the [...] Read more.

Organellar genomes of bryophytes are poorly represented with chloroplast genomes of only four mosses, four liverworts and two hornworts having been sequenced and annotated. Moreover, while Antarctic vegetation is dominated by the bryophytes, there are few reports on the plastid genomes for the Antarctic bryophytes. Sanionia uncinata (Hedw.) Loeske is one of the most dominant moss species in the maritime Antarctic. It has been researched as an important marker for ecological studies and as an extremophile plant for studies on stress tolerance. Here, we report the complete plastome sequence of S. uncinata, which can be exploited in comparative studies to identify the lineage-specific divergence across different species. The complete plastome of S. uncinata is 124,374 bp in length with a typical quadripartite structure of 114 unique genes including 82 unique protein-coding genes, 37 tRNA genes and four rRNA genes. However, two genes encoding the α subunit of RNA polymerase (rpoA) and encoding the cytochrome b_6/f complex subunit VIII (petN) were absent. We could identify nuclear genes homologous to those genes, which suggests that rpoA and petN might have been relocated from the chloroplast genome to the nuclear genome. Full article

(This article belongs to the Special Issue Chloroplast)

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Graphical abstract

Graphical abstract
Full article ">Figure 1
Map of the Sanionia uncinata plastome. Complete plastome sequences were obtained from the de novo assembly of Illumina paired-end reads. Genes are color coded by functional group, which are located in the left box. The inner darker gray circle indicates the GC content while the lighter gray corresponds to AT content. IR, inverted repeat; LSC, large single copy region; SSC, small single copy region. Genes shown on the outside of the outer circle are transcribed clockwise and those on the inside counter clockwise. The map was made with OGDraw [<a href="#B31-ijms-19-00709" class="html-bibr">31</a>]. Full article ">Figure 2
Alignment of complete plastome sequences from six species. Alignment and comparison were performed using mVISTA and the percentage of identity between the plastomes was visualized in the form of an mVISTA plot. The sequence similarity of the aligned regions between S. uncinata and other five species is shown as horizontal bars indicating average percent identity between 50–100% (shown on the y-axis of graph). The x-axis represents the coordinate in the plastome. Genome regions are color-coded for protein-coding (exon), rRNA, tRNA and conserved non-coding sequences (CNS) as the guide at the bottom-left. Full article ">Figure 3
Phylogenetic tree reconstruction of 23 taxa using MEGA7 based on concatenated sequences of 40 protein-coding genes in the plastome. Maximum likelihood (ML) topology is shown with the bootstrap support values (MP/ML) given at nodes. Forty protein-coding sequences were extracted from annotated plastomes found in GenBank [<a href="#B21-ijms-19-00709" class="html-bibr">21</a>] (<a href="http://www.ncbi.nlm.nih.gov" target="_blank">http://www.ncbi.nlm.nih.gov</a>) (<a href="#app1-ijms-19-00709" class="html-app">Table S2</a>). The nucleotide sequences for each gene were translated into amino acids, aligned in MEGA7 and manually adjusted. Nucleotide sequences were aligned by constraining them to the amino acid sequence alignment. Individual gene alignments were then assembled into a single dataset. Full article ">Figure 4
Comparison of the large inversion in the LSC region among six bryophytes plastomes. In comparative LSC region alignment of rpoA, petN coding regions from M. polymorpha, S. uncinata, T. ruralis, T. pellucida and P. patens. The inverted-arrangement of 71 kb fragment was only detected for P. patens. Full article ">Figure 5
Amino acid alignment of (A) nuc-rpoA and (B) nuc-petN genes of S. uncinata with the nuc-rpoA or cp-rpoA and cp-petN genes from other green plants. Identical amino acid residues are boxed in black, other residues are printed in grey. Signal peptide sequences were predicted using SignalP [<a href="#B45-ijms-19-00709" class="html-bibr">45</a>] and shown as double arrow lines and the asterisk. Full article ">

14 pages, 2162 KiB

Open AccessArticle

Complete Chloroplast Genome Sequences of Four Meliaceae Species and Comparative Analyses

by Malte Mader, Birte Pakull, Céline Blanc-Jolivet, Maike Paulini-Drewes, Zoéwindé Henri-Noël Bouda, Bernd Degen, Ian Small and Birgit Kersten

Int. J. Mol. Sci. 2018, 19(3), 701; https://doi.org/10.3390/ijms19030701 - 1 Mar 2018

Cited by 39 | Viewed by 6488

Abstract

The Meliaceae family mainly consists of trees and shrubs with a pantropical distribution. In this study, the complete chloroplast genomes of four Meliaceae species were sequenced and compared with each other and with the previously published Azadirachta indica plastome. The five plastomes are [...] Read more.

The Meliaceae family mainly consists of trees and shrubs with a pantropical distribution. In this study, the complete chloroplast genomes of four Meliaceae species were sequenced and compared with each other and with the previously published Azadirachta indica plastome. The five plastomes are circular and exhibit a quadripartite structure with high conservation of gene content and order. They include 130 genes encoding 85 proteins, 37 tRNAs and 8 rRNAs. Inverted repeat expansion resulted in a duplication of rps19 in the five Meliaceae species, which is consistent with that in many other Sapindales, but different from many other rosids. Compared to Azadirachta indica, the four newly sequenced Meliaceae individuals share several large deletions, which mainly contribute to the decreased genome sizes. A whole-plastome phylogeny supports previous findings that the four species form a monophyletic sister clade to Azadirachta indica within the Meliaceae. SNPs and indels identified in all complete Meliaceae plastomes might be suitable targets for the future development of genetic markers at different taxonomic levels. The extended analysis of SNPs in the matK gene led to the identification of four potential Meliaceae-specific SNPs as a basis for future validation and marker development. Full article

(This article belongs to the Special Issue Chloroplast)

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Graphical abstract

Graphical abstract
Full article ">Figure 1
Gene map of the complete chloroplast genome of Cedrela odorata (GenBank MG724915). The grey arrows indicate the direction of transcription of the two DNA strands. A GC-content graph is depicted within the inner circle. The circle inside the GC content graph marks the 50% threshold. The maps were created using OrganellarGenomeDRAW [<a href="#B22-ijms-19-00701" class="html-bibr">22</a>]. Full article ">Figure 2
Visualization of pairwise alignments of complete cpDNA sequences of four Meliaceae species each with the cpDNA sequence of Azadirachta indica (reference). VISTA-based similarity plots portraying the sequence identity of each of the four Meliacea species with the reference Azadirachta indica are shown. The annotation (protein-encoding genes) is provided for Azadirachta indica on top (based on the related GenBank file; KF986530.1). Plastome regions with the highest diversity between the 5 Meliaceae individuals are marked by blue arrows (top1–3). Further details are provided in the text below. Full article ">Figure 3
Phylogenetic tree (maximum likelihood) based on whole-plastome sequences of five Meliaceae species and Acer buergerianum (outgroup). Bootstrap values (%) are shown above branches. The bootstrap value on the branch separating Azadirachta indica from the other Meliaceae is below 70% and was not shown for this reason. GenBank accession numbers of the plastomes are given in <a href="#ijms-19-00701-t002" class="html-table">Table 2</a>. Full article ">

12 pages, 3022 KiB

Open AccessArticle

Exploring the History of Chloroplast Capture in Arabis Using Whole Chloroplast Genome Sequencing

by Akira Kawabe, Hiroaki Nukii and Hazuka Y. Furihata

Int. J. Mol. Sci. 2018, 19(2), 602; https://doi.org/10.3390/ijms19020602 - 18 Feb 2018

Cited by 33 | Viewed by 4606

Abstract

Chloroplast capture occurs when the chloroplast of one plant species is introgressed into another plant species. The phylogenies of nuclear and chloroplast markers from East Asian Arabis species are incongruent, which indicates hybrid origin and shows chloroplast capture. In the present study, the [...] Read more.

Chloroplast capture occurs when the chloroplast of one plant species is introgressed into another plant species. The phylogenies of nuclear and chloroplast markers from East Asian Arabis species are incongruent, which indicates hybrid origin and shows chloroplast capture. In the present study, the complete chloroplast genomes of A. hirsuta, A. nipponica, and A. flagellosa were sequenced in order to analyze their divergence and their relationships. The chloroplast genomes of A. nipponica and A. flagellosa were similar, which indicates chloroplast replacement. If hybridization causing chloroplast capture occurred once, divergence between recipient species would be lower than between donor species. However, the chloroplast genomes of species with possible hybrid origins, A. nipponica and A. stelleri, differ at similar levels to possible maternal donor species A. flagellosa, which suggests that multiple hybridization events have occurred in their respective histories. The mitochondrial genomes exhibited similar patterns, while A. nipponica and A. flagellosa were more similar to each other than to A. hirsuta. This suggests that the two organellar genomes were co-transferred during the hybridization history of the East Asian Arabis species. Full article

(This article belongs to the Special Issue Chloroplast)

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Figure 1

Figure 1
Chloroplast genome structure of Arabis species. Genes shown outside the map circles are transcribed clockwise, while those drawn inside are transcribed counterclockwise. Genes from different functional groups are color-coded according to the key at the top right. The positions of long single copy (LSC), short single copy (SSC), and two inverted repeat (IR: IRA and IRB) regions are shown in the inner circles. Full article ">Figure 2
Chloroplast genome-based phylogenetic trees of Arabis species. The neighbor-joining trees were constructed using both (A) whole chloroplast genomes and (B) synonymous divergence from concatenated CDS. Numbers beside the nodes indicate bootstrap probabilities (%). Scale bars are shown at the bottom left of each tree. Full article ">Figure 3
Alignment of the seven chloroplast genomes. VISTA-based identity plots of chloroplast genomes from six Arabis species and Draba nemorosa are compared to A. nipponica strain Midori. Arrows above the alignment indicate genes and their orientation. The names of genes ≥500 bp in length are also shown. A 70% identity cut-off was used for making the plots, and the Y-axis represents percent identity (50–100%), while the X-axis represents the location in the chloroplast genome. The blue and pink regions indicate genes and conserved noncoding sequences, respectively. Full article ">

13 pages, 1965 KiB

Open AccessArticle

Effects of TROL Presequence Mutagenesis on Its Import and Dual Localization in Chloroplasts

by Lea Vojta, Andrea Čuletić and Hrvoje Fulgosi

Int. J. Mol. Sci. 2018, 19(2), 569; https://doi.org/10.3390/ijms19020569 - 14 Feb 2018

Cited by 6 | Viewed by 3857

Abstract

Thylakoid rhodanase-like protein (TROL) is involved in the final step of photosynthetic electron transport from ferredoxin to ferredoxin: NADP⁺ oxidoreductase (FNR). TROL is located in two distinct chloroplast compartments—in the inner envelope of chloroplasts, in its precursor form; and in the thylakoid [...] Read more.

Thylakoid rhodanase-like protein (TROL) is involved in the final step of photosynthetic electron transport from ferredoxin to ferredoxin: NADP⁺ oxidoreductase (FNR). TROL is located in two distinct chloroplast compartments—in the inner envelope of chloroplasts, in its precursor form; and in the thylakoid membranes, in its fully processed form. Its role in the inner envelope, as well as the determinants for its differential localization, have not been resolved yet. In this work we created six N-terminal amino acid substitutions surrounding the predicted processing site in the presequence of TROL in order to obtain a construct whose import is affected or localization limited to a single intrachloroplastic site. By using in vitro transcription and translation and subsequent protein import methods, we found that a single amino acid exchange in the presequence, Ala67 to Ile67 interferes with processing in the stroma and directs the whole pool of in vitro translated TROL to the inner envelope of chloroplasts. This result opens up the possibility of studying the role of TROL in the chloroplast inner envelope as well as possible consequence/s of its absence from the thylakoids. Full article

(This article belongs to the Special Issue Chloroplast)

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Graphical abstract

Graphical abstract
Full article ">Figure 1
Kyte and Doolittle plots representing hydrophobicity change as a consequence of amino acid substitution/s in the TROL presequence [<a href="#B23-ijms-19-00569" class="html-bibr">23</a>]. Amino acids 67–78 of the partially conserved N-terminal part of the presequence around the predicted transit peptide cleavage site, AKSLTYEEALQQ, were substituted as follows: e1: 67Ala→67Ile, e2: 71Thr→71Asn, e3: 72Tyr→72Val, e4:73Glu74Glu→73Gln74Gln, e5: 76Leu→76Thr, e6:78Gln→78Val. For the e6 substitution, a polarity check according to Zimmerman was performed [<a href="#B24-ijms-19-00569" class="html-bibr">24</a>]. Full article ">Figure 1 Cont.
Kyte and Doolittle plots representing hydrophobicity change as a consequence of amino acid substitution/s in the TROL presequence [<a href="#B23-ijms-19-00569" class="html-bibr">23</a>]. Amino acids 67–78 of the partially conserved N-terminal part of the presequence around the predicted transit peptide cleavage site, AKSLTYEEALQQ, were substituted as follows: e1: 67Ala→67Ile, e2: 71Thr→71Asn, e3: 72Tyr→72Val, e4:73Glu74Glu→73Gln74Gln, e5: 76Leu→76Thr, e6:78Gln→78Val. For the e6 substitution, a polarity check according to Zimmerman was performed [<a href="#B24-ijms-19-00569" class="html-bibr">24</a>]. Full article ">Figure 2
(A) Wt TROL and its presequence mutants e1–e6 are imported into pea chloroplasts. In vitro synthesized [35S]-TROL and e1–e6, as well as the control protein pOE33 from thylakoid lumen were incubated with isolated intact chloroplasts at 25 °C for 20 min, in a standard import reaction containing 3 mM ATP (lanes 4, 5, 9, and 10) or without ATP (lanes 2, 3, 7, and 8). After import, samples were re-isolated on a Percoll cushion and treated with 0.5 µg thermolysin (Th) per µg chlorophyll (lanes 3, 5, 8, and 10). Untreated samples are shown in lanes 2, 4, 7, and 9. The results were analyzed by SDS⁄PAGE. Lanes 1 and 6 represent 10% of the translation product (Tp) used for the import reactions. The positions of pTROL, mTROL, pOE33, iOE33, and mOE33 are indicated by arrows. (B) Comparison of import of TROL and its presequence mutants e1–e6 into chloroplasts. In vitro synthesized [35S]-TROL and e1–e6 were incubated with isolated intact chloroplasts at 25 °C for 20 min, in a standard import reaction containing 3 mM ATP. After import, samples were re-isolated on a Percoll cushion and treated with 0.5 µg thermolysin (Th) per µg chlorophyll (lanes 2, 4, 6, 8, 10, 12, and 14). The results were analyzed by SDS⁄PAGE. Lanes 1, 3, 5, 7, 9, 11, and 13 represent 10% of the respective translation product. The positions of pTROL and mTROL are indicated by arrows. Full article ">Figure 3
Energy requirement for import of wt TROL and its presequence mutants e1 and e5 into pea chloroplasts. Import into intact pea chloroplasts was performed under standard conditions, by incubating in vitro synthesized [35S]-TROL, e1, e5, and control protein pOE33 from thylakoid lumen with chloroplasts corresponding to 20 µg chlorophyll at 25 °C. ATP-scale import into intact pea chloroplasts was performed using increasing concentrations of ATP from 0 to 3000 µM. After import, chloroplasts were re-isolated on a Percoll cushion and samples were treated with 0.5 µg thermolysin (Th) per µg chlorophyll (lanes 3, 5, 7 and 9). Untreated samples are shown in lanes 2, 4, 6, and 8. The results were analyzed by SDS/PAGE. The respective precursor, intermediate, and mature forms are indicated by arrow heads. Lane 1 represents 1/10 of the translation product (Tp) used for the import reaction. Full article ">Figure 4
Time-scale import of wt TROL and e1 and e5 presequence mutants into intact pea chloroplasts. Radioactively labeled TROL, e1, e5, and control protein pOE33 were imported using increasing times in standard import reactions at 25 °C in the presence of 3 mM ATP. Import was performed for 0.5 (lanes 2 and 3), 2 (lanes 4 and 5), 5 (lanes 6 and 7), 10 (lanes 8 and 9), or 20 min (lanes 10 and 11). After import chloroplasts were separated into the pellet (P, lanes 2, 4, 6, 8, and 10) and soluble (S, lanes 3, 5, 7, 9, and 11) fractions. Lane 1 indicates 1/10 of the respective translation product (Tp) used for the import reaction. Precursor (p), intermediate (i), and mature (m) forms of TROL, e1, e5, and OE33 are indicated by arrows. Full article ">Figure 5
Extraction of wt TROL and its presequence mutants e1 and e5 from the membranes. In vitro synthesized [35S]-TROL, e1, e5, and control protein pOE33 were incubated with isolated intact chloroplasts at 25 °C for 20 min, in a standard import reaction containing 3 mM ATP. Subsequent to import, chloroplasts were re-isolated, washed, and separated into membrane and soluble fractions. Isolated membranes, containing imported proteins, were treated with 6 M Urea in 10 mM HEPES/KOH pH 7.6 (lanes 2 and 3), 0.1 M Na2CO3 pH 11.5 (lanes 4 and 5), or 1 M NaCl (lanes 6 and 7). All incubations were performed for 20 min on RT. As a control, membranes were incubated solely in 10 mM HEPES/KOH pH 7.6 for 30 min on ice (lanes 8 and 9). Afterwards, samples were centrifuged at 265,000× g for 10 min at 4 °C, and both pellets (P, lanes 2, 4, 6, and 8) and the supernatants (S, lanes 3, 5, 7, and 9) were analyzed by SDS–PAGE and by exposure on X-ray films. Lane 1 represents 10% of the respective translation product (Tp) used for the import reactions. The positions of pTROL, mTROL, pOE33, iOE33, and mOE33 are indicated by arrows. Full article ">

18 pages, 3657 KiB

Open AccessArticle

The Complete Chloroplast Genome of Catha edulis: A Comparative Analysis of Genome Features with Related Species

by Cuihua Gu, Luke R. Tembrock, Shaoyu Zheng and Zhiqiang Wu

Int. J. Mol. Sci. 2018, 19(2), 525; https://doi.org/10.3390/ijms19020525 - 9 Feb 2018

Cited by 37 | Viewed by 5463

Abstract

Qat (Catha edulis, Celastraceae) is a woody evergreen species with great economic and cultural importance. It is cultivated for its stimulant alkaloids cathine and cathinone in East Africa and southwest Arabia. However, genome information, especially DNA sequence resources, for C. edulis [...] Read more.

Qat (Catha edulis, Celastraceae) is a woody evergreen species with great economic and cultural importance. It is cultivated for its stimulant alkaloids cathine and cathinone in East Africa and southwest Arabia. However, genome information, especially DNA sequence resources, for C. edulis are limited, hindering studies regarding interspecific and intraspecific relationships. Herein, the complete chloroplast (cp) genome of Catha edulis is reported. This genome is 157,960 bp in length with 37% GC content and is structurally arranged into two 26,577 bp inverted repeats and two single-copy areas. The size of the small single-copy and the large single-copy regions were 18,491 bp and 86,315 bp, respectively. The C. edulis cp genome consists of 129 coding genes including 37 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes, and 84 protein coding genes. For those genes, 112 are single copy genes and 17 genes are duplicated in two inverted regions with seven tRNAs, four rRNAs, and six protein coding genes. The phylogenetic relationships resolved from the cp genome of qat and 32 other species confirms the monophyly of Celastraceae. The cp genomes of C. edulis, Euonymus japonicus and seven Celastraceae species lack the rps16 intron, which indicates an intron loss took place among an ancestor of this family. The cp genome of C. edulis provides a highly valuable genetic resource for further phylogenomic research, barcoding and cp transformation in Celastraceae. Full article

(This article belongs to the Special Issue Chloroplast)

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Figure 1

Figure 1
Circular map of the C. edulis cp genome. Genes shown inside and outside of the outer circle are transcribed clockwise and counterclockwise, respectively. The innermost shaded area inside the inner circle corresponds to GC content in the cp genome. Genes in different functional groups are color coded. IR, inverted repeat; LSC, large single copy region; SSC, small single copy region. The map is drawn using OGDRAW (V 1.2, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Germany). Full article ">Figure 2
Comparison of junctions between the LSC, SSC, and IRs among eight species. Number above indicates the distance in bp between the ends of genes and the borders sites (distances are not to scale in this figure). The ψ symbol represents pseudogenes. Full article ">Figure 3
The sequence variation for rps16 gene with and without intron: (A) The structural components of rps16 gene in 20 species. All Species outside of Celastraceae family contained the rps16 intron. (B) The purple area in all eight species from different genera of the Celastraceae family showed the connection of two exons indicating the lost intron. Full article ">Figure 4
Analysis of repeat sequences in eight chloroplast genomes: (A) frequency of repeat types; and (B) frequency of the repeats by length ≥30 bp. Full article ">Figure 5
The distribution, type, and presence of simple sequence repeats (SSRs) in eight chloroplast genomes: (A) number of different SSR types detected in eight chloroplast genomes presence of SSRs at the LSC, SSC, and IR regions.; (B) frequency of SSRs in the protein-coding regions, intergenic spacers and intronic regions; (C) frequency of SSRs in the LSC, SSC, and IR regions; and (D) frequency of common motifs in the eight chloroplast genomes. Full article ">Figure 6
Phylogenetic tree based on 73 shared protein-coding genes was constructed for 33 species using three different methods, including Parsimony analysis, maximum likelihood (ML) and Bayesian inference (BI). All branches had bootstrap values or posterior probability of 100/1.00 except those labeled. The rps16 gene losses are indicated with green triangles and the rps16 intron loss is indicated with a purple triangle. Full article ">

17 pages, 2608 KiB

Open AccessArticle

Comparative Genomics of the Balsaminaceae Sister Genera Hydrocera triflora and Impatiens pinfanensis

by Zhi-Zhong Li, Josphat K. Saina, Andrew W. Gichira, Cornelius M. Kyalo, Qing-Feng Wang and Jin-Ming Chen

Int. J. Mol. Sci. 2018, 19(1), 319; https://doi.org/10.3390/ijms19010319 - 23 Jan 2018

Cited by 20 | Viewed by 7538

Abstract

The family Balsaminaceae, which consists of the economically important genus Impatiens and the monotypic genus Hydrocera, lacks a reported or published complete chloroplast genome sequence. Therefore, chloroplast genome sequences of the two sister genera are significant to give insight into the phylogenetic [...] Read more.

The family Balsaminaceae, which consists of the economically important genus Impatiens and the monotypic genus Hydrocera, lacks a reported or published complete chloroplast genome sequence. Therefore, chloroplast genome sequences of the two sister genera are significant to give insight into the phylogenetic position and understanding the evolution of the Balsaminaceae family among the Ericales. In this study, complete chloroplast (cp) genomes of Impatiens pinfanensis and Hydrocera triflora were characterized and assembled using a high-throughput sequencing method. The complete cp genomes were found to possess the typical quadripartite structure of land plants chloroplast genomes with double-stranded molecules of 154,189 bp (Impatiens pinfanensis) and 152,238 bp (Hydrocera triflora) in length. A total of 115 unique genes were identified in both genomes, of which 80 are protein-coding genes, 31 are distinct transfer RNA (tRNA) and four distinct ribosomal RNA (rRNA). Thirty codons, of which 29 had A/T ending codons, revealed relative synonymous codon usage values of >1, whereas those with G/C ending codons displayed values of <1. The simple sequence repeats comprise mostly the mononucleotide repeats A/T in all examined cp genomes. Phylogenetic analysis based on 51 common protein-coding genes indicated that the Balsaminaceae family formed a lineage with Ebenaceae together with all the other Ericales. Full article

(This article belongs to the Special Issue Chloroplast)

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Figure 1

Figure 1
Gene map of the Impatiens pinfanensis chloroplast genome. Genes lying outside of the circle are transcribed clockwise, while genes inside the circle are transcribed counterclockwise. The colored bars indicate different functional groups. The dark gray area in the inner circle corresponds to GC content while the light gray corresponds to the adenine-thymine (AT) content of the genome. Full article ">Figure 2
Gene map of the Hydrocera triflora chloroplast genome. Genes lying outside of the circle are transcribed clockwise, while genes inside the circle are transcribed counterclockwise. The colored bars indicate different functional groups. The dark gray area in the inner circle corresponds to (guanine cytosine) GC content while the light gray corresponds to the AT content of the genome. Full article ">Figure 3
Non-synonymous (Ka) and synonymous (Ks) substitution rates and Ka/Ks ratio between I. pinfanensis and H. triflora. One gene psbK had Ka/Ks ratio greater than 1.0, whereas all the other genes were less than 1.0. Full article ">Figure 4
Comparison of IR, LSC and SSC border regions among eight Ericales cp genomes. The IRb/SSC junction extended into the ycf1 genes creating various lengths of ycf1 pseudogenes among the eight cp genomes. The numbers above, below or adjacent to genes shows the distance between the ends of genes and the boundary sites. The figure features are not to scale. ᵠ indicates a pseudogene. Full article ">Figure 5
Phylogenetic relationships based on 51 common protein-coding genes of 38 representative species from order Ericales and four Cornales as Outgroup species with maximum likelihood. The numbers associated with the nodes indicate bootstrap values tested with 1000 replicates. Full article ">

3747 KiB

Open AccessArticle

Mutational Biases and GC-Biased Gene Conversion Affect GC Content in the Plastomes of Dendrobium Genus

by Zhitao Niu, Qingyun Xue, Hui Wang, Xuezhu Xie, Shuying Zhu, Wei Liu and Xiaoyu Ding

Int. J. Mol. Sci. 2017, 18(11), 2307; https://doi.org/10.3390/ijms18112307 - 2 Nov 2017

Cited by 41 | Viewed by 5452

Abstract

The variation of GC content is a key genome feature because it is associated with fundamental elements of genome organization. However, the reason for this variation is still an open question. Different kinds of hypotheses have been proposed to explain the variation of [...] Read more.

The variation of GC content is a key genome feature because it is associated with fundamental elements of genome organization. However, the reason for this variation is still an open question. Different kinds of hypotheses have been proposed to explain the variation of GC content during genome evolution. However, these hypotheses have not been explicitly investigated in whole plastome sequences. Dendrobium is one of the largest genera in the orchid species. Evolutionary studies of the plastomic organization and base composition are limited in this genus. In this study, we obtained the high-quality plastome sequences of D. loddigesii and D. devonianum. The comparison results showed a nearly identical organization in Dendrobium plastomes, indicating that the plastomic organization is highly conserved in Dendrobium genus. Furthermore, the impact of three evolutionary forces—selection, mutational biases, and GC-biased gene conversion (gBGC)—on the variation of GC content in Dendrobium plastomes was evaluated. Our results revealed: (1) consistent GC content evolution trends and mutational biases in single-copy (SC) and inverted repeats (IRs) regions; and (2) that gBGC has influenced the plastome-wide GC content evolution. These results suggest that both mutational biases and gBGC affect GC content in the plastomes of Dendrobium genus. Full article

(This article belongs to the Special Issue Chloroplast)

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Graphical abstract

Graphical abstract
Full article ">Figure 1
Genome map of two newly sequenced Dendrobium plastomes. Only the plastome of D. loddigesii is shown because it has an identical structure with D. devonianum. Genes outside and inside the circle are transcribed clockwise and counterclockwise, respectively. LSC: large single-copy; SSC: small single-copy; IRA and IRB: two identical inverted repeats. Full article ">Figure 2
Dot-plot analysis of the four Dendrobium plastomes. The Dendrobium plastomes appear to have a nearly identical organization, which indicates that their plastomic organization is highly conserved. The black arrows indicate the different loss/retention of ndh genes. Full article ">Figure 3
The BI tree inferred from whole plastome sequences of Dendrobium species. Tree node labeled with “A” denotes to the ancestor for each Dendrobium species. The values of posterior probabilities are showed for each node. Full article ">Figure 4
Proportion of the six nucleotide-pair mutations estimated from non-coding loci of the SC and IR regions of 10 Dendrobium species. The numbers of A to G mutations are normalized for the unequal nucleotide content of Dendrobium species. The frequencies of transversions are higher than that of transitions in both SC and IR regions. Full article ">Figure 4 Cont.
Proportion of the six nucleotide-pair mutations estimated from non-coding loci of the SC and IR regions of 10 Dendrobium species. The numbers of A to G mutations are normalized for the unequal nucleotide content of Dendrobium species. The frequencies of transversions are higher than that of transitions in both SC and IR regions. Full article ">Figure 5
Comparison of equilibrium GC content (GCeq) values between the SC and IR regions for the non-coding regions. Error bars depict 95% confidence intervals for GCeq. Note that, the non-coding regions showed contrast GCeq values (<50% in SC and >50% in IR) in SC and IR regions. Moreover, the estimated GCeq values are lower than current GC content in SC regions, but higher than current GC content in IR regions. Full article ">Figure 6
Proportion of the six nucleotide-pair mutations estimated from protein-coding genes. In contrast to the counting results of non-coding loci, the frequencies of transitions are higher than that of transversions in both SC and IR regions. Full article ">Figure 7
Comparison of GCeq values between the SC and IR regions for the protein-coding genes. Error bars depict 95% confidence intervals for GCeq. The protein-coding genes showed the same evolution trends with the non-coding loci. Full article ">

2431 KiB

Open AccessArticle

The Complete Chloroplast Genome Sequences of the Medicinal Plant Forsythia suspensa (Oleaceae)

by Wenbin Wang, Huan Yu, Jiahui Wang, Wanjun Lei, Jianhua Gao, Xiangpo Qiu and Jinsheng Wang

Int. J. Mol. Sci. 2017, 18(11), 2288; https://doi.org/10.3390/ijms18112288 - 31 Oct 2017

Cited by 88 | Viewed by 7113

Abstract

Forsythia suspensa is an important medicinal plant and traditionally applied for the treatment of inflammation, pyrexia, gonorrhea, diabetes, and so on. However, there is limited sequence and genomic information available for F. suspensa. Here, we produced the complete chloroplast genomes of F. [...] Read more.

Forsythia suspensa is an important medicinal plant and traditionally applied for the treatment of inflammation, pyrexia, gonorrhea, diabetes, and so on. However, there is limited sequence and genomic information available for F. suspensa. Here, we produced the complete chloroplast genomes of F. suspensa using Illumina sequencing technology. F. suspensa is the first sequenced member within the genus Forsythia (Oleaceae). The gene order and organization of the chloroplast genome of F. suspensa are similar to other Oleaceae chloroplast genomes. The F. suspensa chloroplast genome is 156,404 bp in length, exhibits a conserved quadripartite structure with a large single-copy (LSC; 87,159 bp) region, and a small single-copy (SSC; 17,811 bp) region interspersed between inverted repeat (IRa/b; 25,717 bp) regions. A total of 114 unique genes were annotated, including 80 protein-coding genes, 30 tRNA, and four rRNA. The low GC content (37.8%) and codon usage bias for A- or T-ending codons may largely affect gene codon usage. Sequence analysis identified a total of 26 forward repeats, 23 palindrome repeats with lengths >30 bp (identity > 90%), and 54 simple sequence repeats (SSRs) with an average rate of 0.35 SSRs/kb. We predicted 52 RNA editing sites in the chloroplast of F. suspensa, all for C-to-U transitions. IR expansion or contraction and the divergent regions were analyzed among several species including the reported F. suspensa in this study. Phylogenetic analysis based on whole-plastome revealed that F. suspensa, as a member of the Oleaceae family, diverged relatively early from Lamiales. This study will contribute to strengthening medicinal resource conservation, molecular phylogenetic, and genetic engineering research investigations of this species. Full article

(This article belongs to the Special Issue Chloroplast)

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Figure 1

Figure 1
Chloroplast genome map of Forsythia suspensa. Genes drawn inside the circle are transcribed clockwise, and those outside are counterclockwise. Genes are color-coded based on their function, which are shown at the left bottom. The inner circle indicates the inverted boundaries and GC content. Full article ">Figure 2
Comparisons of LSC, SSC, and IR region borders among six Lamiales chloroplast genomes. Ψ indicates a pseudogene. Colorcoding mean different genes on both sides of the junctions. Number above the gene features means the distance between the ends of genes and the junction sites. The arrows indicated the location of the distance. This figure is not to scale. Full article ">Figure 3
Distribution of repeat sequence and simple sequence repeats (SSRs) within F. suspensa chloroplast genomes. (A) Distribution of repeats; and (B) distribution of SSRs. IGS: intergenic spacer. Full article ">Figure 4
Maximum likelihood phylogeny of the Lamiales species inferred from complete chloroplast genome sequences. Numbers near branches are bootstrap values of 100 pseudo-replicates. The tree on the right panel was constructed manually by reference to the left one, and the distance of branches was meaningless. The branches without numbers indicate 100% bootstrap supports. Full article ">

3611 KiB

Open AccessArticle

Stable Membrane-Association of mRNAs in Etiolated, Greening and Mature Plastids

by Julia Legen and Christian Schmitz-Linneweber

Int. J. Mol. Sci. 2017, 18(9), 1881; https://doi.org/10.3390/ijms18091881 - 31 Aug 2017

Cited by 6 | Viewed by 3937

Abstract

Chloroplast genes are transcribed as polycistronic precursor RNAs that give rise to a multitude of processing products down to monocistronic forms. Translation of these mRNAs is realized by bacterial type 70S ribosomes. A larger fraction of these ribosomes is attached to chloroplast membranes. [...] Read more.

Chloroplast genes are transcribed as polycistronic precursor RNAs that give rise to a multitude of processing products down to monocistronic forms. Translation of these mRNAs is realized by bacterial type 70S ribosomes. A larger fraction of these ribosomes is attached to chloroplast membranes. This study analyzed transcriptome-wide distribution of plastid mRNAs between soluble and membrane fractions of purified plastids using microarray analyses and validating RNA gel blot hybridizations. To determine the impact of light on mRNA localization, we used etioplasts, greening plastids and mature chloroplasts from Zea mays as a source for membrane and soluble extracts. The results show that the three plastid types display an almost identical distribution of RNAs between the two organellar fractions, which is confirmed by quantitative RNA gel blot analyses. Furthermore, they reveal that different RNAs processed from polycistronic precursors show transcript-autonomous distribution between stroma and membrane fractions. Disruption of ribosomes leads to release of mRNAs from membranes, demonstrating that attachment is likely a direct consequence of translation. We conclude that plastid mRNA distribution is a stable feature of different plastid types, setting up rapid chloroplast translation in any plastid type. Full article

(This article belongs to the Special Issue Chloroplast)

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Figure 1

Figure 1
Enrichment of marker proteins in chloroplast membrane and stroma fractions. Western blot analysis was performed from each type of tissue using RbcL and PetD antisera as markers for stroma and membrane, respectively. RNAs from these fractions were used for microarray analysis. A seven hundredth of each sample was analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The membrane fraction was washed five times prior to RNA extraction. Aliquots from the supernatants of the first and the last wash were analyzed here as well (W1 and W5). Full article ">Figure 2
Microarray analysis of RNAs enriched at chloroplast membranes. (a) Membrane-enrichment of RNA along the chloroplast chromosome. Isolated chloroplast from maize seedlings grown at three different light regimes (leading to mature, greening, and etiolated plastids, respectively) were processed into stroma and membrane fractions. Two µg of RNA isolated from each fraction were differentially labeled and hybridized to a microarray representing the maize chloroplast genome in a tiling fashion. The ratio of membrane versus stroma signal was plotted against the genomic position on the Zea mays chloroplast genome (acc. NC_001666). The graphs shown represent four biological replicates. Normalization between conditions is based on the sum of membrane enrichment values (MEVs) of all probes for each condition. Probes corresponding to mRNAs coding for known membrane proteins are highlighted by dashed boxes. Selected soluble RNAs are labelled as well. The data underlying this chart are deposited in <a href="#app1-ijms-18-01881" class="html-app">Table S1</a>; (b) Gene ontology (GO) term analysis of membrane-enriched RNAs in the chloroplast. The probes showing the top 10 percent MEVs binned into 12 functional categories (PSI = photosystem I; PSII = photosystem II; Prot. = proteins; ORFs = open reading frames of unknown function; misc. = miscellaneous). Probes covering more than one category were counted in each relevant bin. The numbers of probes within each bin are expressed as the fraction of the total number of probes for each condition (in %). This is compared to the distribution of all probes on the array across the bins (open bars). Probes for photosystems I and II are over-represented in the top 10% MEV probes of all three tissue types. Full article ">Figure 3
RNAs are associated to chloroplast membranes via translating ribosomes. (a) Disruption of ribosomes by ethylenediaminetetraacetic acid (EDTA) releases psbD mRNAs into the soluble fraction. Membrane fractions from the same number of plastids from three different tissue types were either treated with EDTA in order to separate the large and small subunit of the ribosome or were treated with buffer (mock). Membranes were spun down after treatment (P) and the supernatant was collected as well (S). RNA was extracted from all fractions and fractionated on 1.2% agarose gel and analyzed by hybridization to a radiolabeled psbD probe (see <a href="#app1-ijms-18-01881" class="html-app">Table S4</a> for primer sequences). As a quality control, the rRNAs were stained with methylene blue; (b) Release of mRNAs from chloroplast membranes after puromycin treatment. Membranes were isolated from mature chloroplasts that were purified from four-week-old plants grown under long-day conditions. Membranes were treated with puromycin to release nascent chains and ribosomes from the mRNAs and thus secondarily free mRNAs from the membrane. The membrane was washed multiple times. RNA from the supernatant after puromycin treatment and from the washed membranes was analyzed by a whole genome tiling array of the maize chloroplast genome. The ratio of freed RNA over membrane-bound RNA was calculated for each probe and plotted against genome position. Selected probes are labelled by the gene-names they represent. The isoaceptor tRNAs are named by their respective codon (GGU, GCA, UGU, CAU and GAC, respectively). Full article ">Figure 4
Analysis of transcript accumulation in membrane and stroma preparations on a per-chloroplast base. Equal aliquots of RNA from membrane and stroma fractions of purified plastids from three different tissues were extracted from the same number of chloroplasts. In addition, five micrograms of total leaf RNA was analyzed as well. The RNAs were fractionated on 1.2% agarose gel and analyzed by hybridization to radiolabeled probes for the plastid RNAs indicated (see <a href="#app1-ijms-18-01881" class="html-app">Table S4</a> for primer sequences). As a quality control, the rRNAs were stained with methylene blue. Str = RNA from stroma fractions; m = RNA from membrane fractions. Full article ">

3809 KiB

Open AccessArticle

Molecular Structure and Phylogenetic Analyses of Complete Chloroplast Genomes of Two Aristolochia Medicinal Species

by Jianguo Zhou, Xinlian Chen, Yingxian Cui, Wei Sun, Yonghua Li, Yu Wang, Jingyuan Song and Hui Yao

Int. J. Mol. Sci. 2017, 18(9), 1839; https://doi.org/10.3390/ijms18091839 - 24 Aug 2017

Cited by 87 | Viewed by 7033

Abstract

The family Aristolochiaceae, comprising about 600 species of eight genera, is a unique plant family containing aristolochic acids (AAs). The complete chloroplast genome sequences of Aristolochia debilis and Aristolochia contorta are reported here. The results show that the complete chloroplast genomes of A. [...] Read more.

The family Aristolochiaceae, comprising about 600 species of eight genera, is a unique plant family containing aristolochic acids (AAs). The complete chloroplast genome sequences of Aristolochia debilis and Aristolochia contorta are reported here. The results show that the complete chloroplast genomes of A. debilis and A. contorta comprise circular 159,793 and 160,576 bp-long molecules, respectively and have typical quadripartite structures. The GC contents of both species were 38.3% each. A total of 131 genes were identified in each genome including 85 protein-coding genes, 37 tRNA genes, eight rRNA genes and one pseudogene (ycf1). The simple-sequence repeat sequences mainly comprise A/T mononucletide repeats. Phylogenetic analyses using maximum parsimony (MP) revealed that A. debilis and A. contorta had a close phylogenetic relationship with species of the family Piperaceae, as well as Laurales and Magnoliales. The data obtained in this study will be beneficial for further investigations on A. debilis and A. contorta from the aspect of evolution, and chloroplast genetic engineering. Full article

(This article belongs to the Special Issue Chloroplast)

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Graphical abstract

Graphical abstract
Full article ">Figure 1
Gene map of the complete chloroplast genome of A. debilis. Genes on the inside of the circle are transcribed clockwise, while those outside are transcribed counter clockwise. The darker gray in the inner circle corresponds to GC content, whereas the lighter gray corresponds to AT content. Full article ">Figure 2
Gene map of the complete chloroplast genome of A. contorta. Genes on the inside of the circle are transcribed clockwise, while those outside are transcribed counter clockwise. The darker gray in the inner circle corresponds to GC content, whereas the lighter gray corresponds to AT content. Full article ">Figure 3
Comparison of the borders of LSC, SSC and IR regions among four chloroplast genomes. Number above the gene features means the distance between the ends of genes and the borders sites. The IRb/SSC border extended intothe ycf1 genes to create various lengths of ycf1 pseudogenes among four chloroplast genomes. These features are not to scale. Full article ">Figure 4
Codon content of 20 amino acid and stop codons in all protein-coding genes of the chloroplast genomes of two Aristolochia species. The histogram on the left-hand side of each amino acid shows codon usage within the A. debilis chloroplast genome, while the right-hand side illustrates the genome of A. contorta. Full article ">Figure 5
Repeat sequences in six chloroplast genomes. REPuter was used to identify repeat sequences with length ≥30 bp and sequence identified ≥90% in the chloroplast genomes. F, P, R, and C indicate the repeat types F (forward), P (palindrome), R (reverse), and C (complement), respectively. Repeats with different lengths are indicated in different colours. Full article ">Figure 6
Sequence identity plot comparing the five chloroplast genomes with A. debilis as a reference by using mVISTA. Grey arrows and thick black lines above the alignment indicate genes with their orientation and the position of the IRs, respectively. A cut-off of 70% identity was used for the plots, and the Y-scale represents the percent identity ranging from 50% to 100%. Full article ">Figure 7
Phylogenetic tree constructed using Maximum parsimony (MP) method based on 60 protein-coding genes from different species. Numbers at nodes are values for bootstrap support. Full article ">

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22 pages, 807 KiB

Open AccessReview

Metabolic Reprogramming in Chloroplasts under Heat Stress in Plants

by Qing-Long Wang, Juan-Hua Chen, Ning-Yu He and Fang-Qing Guo

Int. J. Mol. Sci. 2018, 19(3), 849; https://doi.org/10.3390/ijms19030849 - 14 Mar 2018

Cited by 210 | Viewed by 17106

Abstract

Increases in ambient temperatures have been a severe threat to crop production in many countries around the world under climate change. Chloroplasts serve as metabolic centers and play a key role in physiological adaptive processes to heat stress. In addition to expressing heat [...] Read more.

Increases in ambient temperatures have been a severe threat to crop production in many countries around the world under climate change. Chloroplasts serve as metabolic centers and play a key role in physiological adaptive processes to heat stress. In addition to expressing heat shock proteins that protect proteins from heat-induced damage, metabolic reprogramming occurs during adaptive physiological processes in chloroplasts. Heat stress leads to inhibition of plant photosynthetic activity by damaging key components functioning in a variety of metabolic processes, with concomitant reductions in biomass production and crop yield. In this review article, we will focus on events through extensive and transient metabolic reprogramming in response to heat stress, which included chlorophyll breakdown, generation of reactive oxygen species (ROS), antioxidant defense, protein turnover, and metabolic alterations with carbon assimilation. Such diverse metabolic reprogramming in chloroplasts is required for systemic acquired acclimation to heat stress in plants. Full article

(This article belongs to the Special Issue Chloroplast)

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Figure 1
Extensive and transient metabolic reprogramming in chloroplasts under heat stress. Major events of metabolic reprogramming in response to heat stress include chlorophyll breakdown, generation of reactive oxygen species (ROS), antioxidant defense, protein turnover, and metabolic alterations with carbon assimilation. With respect to the systemic acquired acclimation to heat stress in plants, diverse metabolic reprogramming in chloroplasts is required for optimizing plant growth and development during high temperature stresses. Full article ">Figure 2
A representative scheme of reactive oxygen species (ROS) generation and scavenging in chloroplasts under heat stress. High temperature stress triggers oxidative bursts of superoxide and/or hydrogen peroxide in plants. The transfer of excitation energy in the photosystem II (PSII) antenna complex and the electron transport in the PSII reaction center can be inhibited by heat stress. It has been established that ROS are generated both on the electron acceptor and the electron donor side of PSII under heat stress during which electron transport from the manganese complex to plastoquinone (PQ) is limited. The leakage of electrons to molecular oxygen on the electron acceptor side of PSII forms O2•−, inducing initiation of a cascade reaction leading to the formation of H2O2. A diversified ROS-scavenging network functions in concert in chloroplasts, mainly including antioxidants and APX-glutathione cycle, to keep the equilibrium between ROS production and scavenging. The efficient enzymatic scavenging systems are composed of several key enzymes, including superoxide dismutase (SOD), ascorbate peroxidase (APX), glutathione reductase (GR), monodehydroascorbate reductase (MDHAR), dehydroascorbate reductase (DHAR), glutathione peroxidase (GPX) and glutathione-S-transferase (GST) and non-enzymatic systems contain antioxidants such as ascorbic acid (Asc) and glutathione (GSH). Full article ">

15 pages, 1686 KiB

Open AccessReview

Chloroplast Protein Turnover: The Influence of Extraplastidic Processes, Including Autophagy

by Masanori Izumi and Sakuya Nakamura

Int. J. Mol. Sci. 2018, 19(3), 828; https://doi.org/10.3390/ijms19030828 - 12 Mar 2018

Cited by 50 | Viewed by 6480

Abstract

Most assimilated nutrients in the leaves of land plants are stored in chloroplasts as photosynthetic proteins, where they mediate CO₂ assimilation during growth. During senescence or under suboptimal conditions, chloroplast proteins are degraded, and the amino acids released during this process are [...] Read more.

Most assimilated nutrients in the leaves of land plants are stored in chloroplasts as photosynthetic proteins, where they mediate CO₂ assimilation during growth. During senescence or under suboptimal conditions, chloroplast proteins are degraded, and the amino acids released during this process are used to produce young tissues, seeds, or respiratory energy. Protein degradation machineries contribute to the quality control of chloroplasts by removing damaged proteins caused by excess energy from sunlight. Whereas previous studies revealed that chloroplasts contain several types of intraplastidic proteases that likely derived from an endosymbiosed prokaryotic ancestor of chloroplasts, recent reports have demonstrated that multiple extraplastidic pathways also contribute to chloroplast protein turnover in response to specific cues. One such pathway is autophagy, an evolutionarily conserved process that leads to the vacuolar or lysosomal degradation of cytoplasmic components in eukaryotic cells. Here, we describe and contrast the extraplastidic pathways that degrade chloroplasts. This review shows that diverse pathways participate in chloroplast turnover during sugar starvation, senescence, and oxidative stress. Elucidating the mechanisms that regulate these pathways will help decipher the relationship among the diverse pathways mediating chloroplast protein turnover. Full article

(This article belongs to the Special Issue Chloroplast)

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Figure 1
Schematic model for the Rubisco-containing body (RCB) pathway and chlorophagy forms of chloroplast-related autophagy. (a) When photosynthetic energy production of whole plants is impaired due to complete darkness, a portion of the chloroplast stroma is transported to the central vacuole via RCBs, which are a type of autophagic compartment that specifically contains stromal proteins. The RCB pathway can facilitate the recycling of amino acids as an energy source. (b) When senescence is accelerated in individually darkened leaves, the active production of RCBs leads to chloroplast shrinkage, thereby allowing the transport of entire chloroplasts to the vacuole via chlorophagy. (c) Photodamage from exposure to ultraviolet-B (UV-B), strong visible light, or natural sunlight causes chloroplasts to collapse. The collapsed chloroplasts are then transported to the vacuole without prior activation of RCBs. This process is suggested to serve as a quality control mechanism that removes damaged chloroplasts. Full article ">Figure 2
Schematic model for chloroplast protein turnover mediated by ATI bodies, CV-containing vesicles (CCVs), senescence-associated vacuoles (SAVs), or ubiquitination. (a) Plastid-associated ATI bodies are produced in chloroplasts and are then delivered into the central vacuole via an autophagy-dependent pathway. ATI bodies transport thylakoid, stroma, and envelope proteins. CV protein also interacts with thylakoid and stroma proteins, and then induces the production of CCVs that transport thylakoid, stroma, and envelope proteins into the central vacuole via an autophagy-independent pathway. SAVs are small lytic compartments that form in the cytoplasm. Stroma components are incorporated into the SAVs for digestion. (b) Chloroplast outer envelope-anchored E3 ligase, SP1, ubiquitinates TOC proteins and facilitates their degradation by 26S proteasome. Cytoplasmic E3 ligase PUB4 ubiquitinates oxidative chloroplasts accumulating 1O2 for the digestion of such chloroplasts in their entirety. Full article ">

13 pages, 3772 KiB

Open AccessReview

Insights into the Mechanisms of Chloroplast Division

by Yamato Yoshida

Int. J. Mol. Sci. 2018, 19(3), 733; https://doi.org/10.3390/ijms19030733 - 4 Mar 2018

Cited by 14 | Viewed by 6972

Abstract

The endosymbiosis of a free-living cyanobacterium into an ancestral eukaryote led to the evolution of the chloroplast (plastid) more than one billion years ago. Given their independent origins, plastid proliferation is restricted to the binary fission of pre-existing plastids within a cell. In [...] Read more.

The endosymbiosis of a free-living cyanobacterium into an ancestral eukaryote led to the evolution of the chloroplast (plastid) more than one billion years ago. Given their independent origins, plastid proliferation is restricted to the binary fission of pre-existing plastids within a cell. In the last 25 years, the structure of the supramolecular machinery regulating plastid division has been discovered, and some of its component proteins identified. More recently, isolated plastid-division machineries have been examined to elucidate their structural and mechanistic details. Furthermore, complex studies have revealed how the plastid-division machinery morphologically transforms during plastid division, and which of its component proteins play a critical role in generating the contractile force. Identifying the three-dimensional structures and putative functional domains of the component proteins has given us hints about the mechanisms driving the machinery. Surprisingly, the mechanisms driving plastid division resemble those of mitochondrial division, indicating that these division machineries likely developed from the same evolutionary origin, providing a key insight into how endosymbiotic organelles were established. These findings have opened new avenues of research into organelle proliferation mechanisms and the evolution of organelles. Full article

(This article belongs to the Special Issue Chloroplast)

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13 pages, 1258 KiB

Open AccessReview

Bacterial Heterologous Expression System for Reconstitution of Chloroplast Inner Division Ring and Evaluation of Its Contributors

by Hiroki Irieda and Daisuke Shiomi

Int. J. Mol. Sci. 2018, 19(2), 544; https://doi.org/10.3390/ijms19020544 - 11 Feb 2018

Cited by 3 | Viewed by 4962

Abstract

Plant chloroplasts originate from the symbiotic relationship between ancient free-living cyanobacteria and ancestral eukaryotic cells. Since the discovery of the bacterial derivative FtsZ gene—which encodes a tubulin homolog responsible for the formation of the chloroplast inner division ring (Z ring)—in the Arabidopsis genome [...] Read more.

Plant chloroplasts originate from the symbiotic relationship between ancient free-living cyanobacteria and ancestral eukaryotic cells. Since the discovery of the bacterial derivative FtsZ gene—which encodes a tubulin homolog responsible for the formation of the chloroplast inner division ring (Z ring)—in the Arabidopsis genome in 1995, many components of the chloroplast division machinery were successively identified. The knowledge of these components continues to expand; however, the mode of action of the chloroplast dividing system remains unknown (compared to bacterial cell division), owing to the complexities faced in in planta analyses. To date, yeast and bacterial heterologous expression systems have been developed for the reconstitution of Z ring-like structures formed by chloroplast FtsZ. In this review, we especially focus on recent progress of our bacterial system using the model bacterium Escherichia coli to dissect and understand the chloroplast division machinery—an evolutionary hybrid structure composed of both bacterial (inner) and host-derived (outer) components. Full article

(This article belongs to the Special Issue Chloroplast)

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Figure 1
The formation of Z ring-like structures of Arabidopsis chloroplast FtsZ2 in the bacterial heterologous expression system. Schematic illustration of the proposed molecular behavior of chloroplast division-related components in E. coli cells and its merged microscopic image of phase-contrast and GFP are shown when expressing (a) super folder GFP (sfGFP)-AtFtsZ2, (b) sfGFP-AtFtsZ2-2MTS, (c) sfGFP-AtFtsZ2, and Accumulation and Replication of Chloroplasts 6 (ARC6) and (d) sfGFP-AtFtsZ2∆C18 (C-terminal 18-residue truncated form of AtFtsZ2) and ARC6. E. coli cells were grown in L broth (1% bactotryptone, 0.5% yeast extract, 0.5% NaCl) to the stationary phase at 22 °C. Scale bars: 5 µm. MTS: membrane-targeting sequence. To reduce the complexity in the diagrams, bundling of the FtsZ2 filaments was omitted. Full article ">Figure 2
The effects of Accumulation and Replication of Chloroplasts 3 (ARC3) on the filaments of Arabidopsis chloroplast FtsZ2 in the bacterial heterologous expression system. Schematic illustration of the proposed molecular behavior of chloroplast division-related components in E. coli cells and its merged microscopic image of phase-contrast and GFP are shown when expressing (a) sfGFP-AtFtsZ2 and ARC3, and (b) sfGFP-AtFtsZ2-2MTS and ARC3. E. coli cells were grown in L broth (1% bactotryptone, 0.5% yeast extract, 0.5% NaCl) to the stationary phase at 22 °C. Scale bars: 5 µm. MTS: membrane-targeting sequence. To reduce the complexity in the diagrams, bundling of the FtsZ2 filaments was omitted. Full article ">Figure 3
The effects of Arabidopsis chloroplast FtsZ1 on the formation of Z ring-like structures of Arabidopsis chloroplast FtsZ2 in the bacterial heterologous expression system. Schematic illustration of the Z ring-like structures composed of AtFtsZ1 and AtFtsZ2 heterooligomer in E. coli cells, although the mechanism by which the Arabidopsis FtsZ filaments are tethered to the membrane is unclear (indicated by red question marks in the illustration), and its merged microscopic images of phase-contrast and GFP (upper panel), and phase-contrast and mCherry (lower panel) are shown. E. coli cells expressing sfGFP-AtFtsZ2 and mCherry-AtFtsZ1 were grown in L broth (1% bactotryptone, 0.5% yeast extract, 0.5% NaCl) to the stationary phase at 22 °C. Scale bar: 5 µm. To reduce the complexity in the diagram, bundling of the FtsZ filaments was omitted. Full article ">

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Open AccessBrief Report

A Simple Method to Decode the Complete 18-5.8-28S rRNA Repeated Units of Green Algae by Genome Skimming

by Geng-Ming Lin, Yu-Heng Lai, Gilbert Audira and Chung-Der Hsiao

Int. J. Mol. Sci. 2017, 18(11), 2341; https://doi.org/10.3390/ijms18112341 - 6 Nov 2017

Cited by 6 | Viewed by 6226

Abstract

Green algae, Chlorella ellipsoidea, Haematococcus pluvialis and Aegagropila linnaei (Phylum Chlorophyta) were simultaneously decoded by a genomic skimming approach within 18-5.8-28S rRNA region. Whole genomic DNAs were isolated from green algae and directly subjected to low coverage genome skimming sequencing. After de [...] Read more.

Green algae, Chlorella ellipsoidea, Haematococcus pluvialis and Aegagropila linnaei (Phylum Chlorophyta) were simultaneously decoded by a genomic skimming approach within 18-5.8-28S rRNA region. Whole genomic DNAs were isolated from green algae and directly subjected to low coverage genome skimming sequencing. After de novo assembly and mapping, the size of complete 18-5.8-28S rRNA repeated units for three green algae were ranged from 5785 to 6028 bp, which showed high nucleotide diversity (π is around 0.5–0.6) within ITS1 and ITS2 (Internal Transcribed Spacer) regions. Previously, the evolutional diversity of algae has been difficult to decode due to the inability design universal primers that amplify specific marker genes across diverse algal species. In this study, our method provided a rapid and universal approach to decode the 18-5.8-28S rRNA repeat unit in three green algal species. In addition, the completely sequenced 18-5.8-28S rRNA repeated units provided a solid nuclear marker for phylogenetic and evolutionary analysis for green algae for the first time. Full article

(This article belongs to the Special Issue Chloroplast)

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Two Coiled-Coil Proteins, WEB1 and PMI2, Suppress the Signaling Pathway of Chloroplast Accumulation Response that Is Mediated by Two Phototropin-Interacting Proteins, RPT2 and NCH1, in Seed Plants

by Noriyuki Suetsugu and Masamitsu Wada

Int. J. Mol. Sci. 2017, 18(7), 1469; https://doi.org/10.3390/ijms18071469 - 8 Jul 2017

Cited by 4 | Viewed by 4389

Abstract

Chloroplast movement is induced by blue light in a broad range of plant species. Weak light induces the chloroplast accumulation response and strong light induces the chloroplast avoidance response. Both responses are essential for efficient photosynthesis and are mediated by phototropin blue-light receptors. [...] Read more.

Chloroplast movement is induced by blue light in a broad range of plant species. Weak light induces the chloroplast accumulation response and strong light induces the chloroplast avoidance response. Both responses are essential for efficient photosynthesis and are mediated by phototropin blue-light receptors. J-DOMAIN PROTEIN REQUIRED FOR CHLOROPLAST ACCUMULATION RESPONSE 1 (JAC1) and two coiled-coil domain proteins WEAK CHLOROPLAST MOVEMENT UNDER BLUE LIGHT 1 (WEB1) and PLASTID MOVEMENT IMPAIRED 2 (PMI2) are required for phototropin-mediated chloroplast movement. Genetic analysis suggests that JAC1 is essential for the accumulation response and WEB1/PMI2 inhibit the accumulation response through the suppression of JAC1 activity under the strong light. We recently identified two phototropin-interacting proteins, ROOT PHOTOTROPISM 2 (RPT2) and NPH3/RPT2-like (NRL) PROTEIN FOR CHLOROPLAST MOVEMENT 1 (NCH1) as the signaling components involved in chloroplast accumulation response. However, the relationship between RPT2/NCH1, JAC1 and WEB1/PMI2 remained to be determined. Here, we performed genetic analysis between RPT2/NCH1, JAC1, and WEB1/PMI2 to elucidate the signal transduction pathway. Full article

(This article belongs to the Special Issue Chloroplast)

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Figure 1
(a) Protein structure of ROOT PHOTOTROPISM 2 (RPT2), NRL PROTEIN FOR CHLOROPLAST MOVEMENT 1 (NCH1), J-DOMAIN PROTEIN REQUIRED FOR CHLOROPLAST ACCUMULATION RESPONSE 1 (JAC1), WEAK CHLOROPLAST MOVEMENT UNDER BLUE LIGHT 1 (WEB1), and PLASTID MOVEMENT IMPAIRED 2 (PMI2). Blue boxes indicate the four conserved regions of NPH3/RPT2-like (NRL) proteins. The position of the BTB/POZ domain is indicated by a black bar. Red box is a J-domain. Green boxes indicate the coiled-coil domains; (b) Measurement of light-induced changes in leaf transmittance as a result of chloroplast photorelocation movements. The depicted trace represents typical data collected for wild type under the various light irradiation conditions (indicated by color boxes). There is a decrease in leaf transmittance in response to 3 μmol m−2 s−1 of blue light, indicating that the accumulation response is induced (downward arrow). Conversely, there is an increase in leaf transmittance in response to 20 and 50 μmol m−2 s−1 of blue light, indicating that the avoidance response is induced (upward arrows). Red lines mark the initial linear fragments of leaf transmittance rate change during the first 2–6 min of the irradiation period, indicating the velocity. A red parenthesis marks the difference between the transmittance level observed following 60 min of 3 μmol m−2 s−1 blue-light irradiation and the transmittance level observed a following further 40 min of 20 μmol m−2 s−1 blue-light irradiation, indicating the amplitude of the avoidance response caused by 20 μmol m−2 s−1 blue-light irradiation; (c–e) Distinct chloroplast movements observed between rpt2nch1 and jac1; (c) Light-induced changes in leaf transmittance of the indicated lines were measured using a custom-made plate reader system [<a href="#B14-ijms-18-01469" class="html-bibr">14</a>]. The samples were sequentially irradiated with 3, 20 and 50 μmol m−2 s−1 of continuous blue light. The beginning of each irradiation period is indicated by white, cyan and blue arrows, respectively. The light was extinguished after 150 min (black arrow); (d) The velocity of light-induced transmittance changes. (e) The amplitude of the avoidance response caused by 20 μmol m−2 s−1 blue-light irradiation. Data for wild type, rpt2nch1, jac1 and rpt2nch1jac1 from Suetsugu et al. (2016) [<a href="#B12-ijms-18-01469" class="html-bibr">12</a>] were used for comparison, because data for web1, rpt2nch1web1, pmi2pmi15 and rpt2nch1pmi2pmi15 were acquired in the same experiments using the same plate. Data are presented as means of three independent experiments and the error bars indicate standard errors. WT, wild type. Full article ">Figure 2
Working model of chloroplast photorelocation movements. The photoreceptors phot1 and phot2 mediate the accumulation response under a low light condition through RPT2 and NCH1. RPT2 and NCH1 might regulate both JAC1-dependent and -independent (X) pathways. The signaling pathway by RPT2/NCH1 and JAC1 suppresses that of the avoidance response under a low light condition. Under the high light condition, the WEB1/PMI2 complex suppresses the signaling pathway for the accumulation response that is regulated by RPT2/NCH1 and JAC1 through an unknown mechanism, resulting in the efficient induction of the avoidance response mediated by phot2. Gray arrows indicate the suppressed signaling pathways. Black arrows indicate the activated signaling pathways. Full article ">

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