Search Results (714)

The genus Borodinellopsis is extremely rare and is the subject of limited research and reports. It currently comprises only two species, Borodinellopsis texensis and Borodinellopsis oleifera, which differ from other globose algae due to their unique centrally radiating chloroplasts. In this study, we describe a new specimen in detail based on morphological data and phylogenetic analysis and identify it as B. insignis. B. insignis and B. texensis exhibit a high degree of similarity, likely due to their shared characteristics of centrally radiating chloroplasts and flagella that are significantly longer than the cell body. A phylogenetic tree constructed based on the 18S rDNA sequence indicates that B. insignis and B. texensis form a branch that is distinct from other genera, such as Tetracystis, Spongiococcum, and Chlorococcum. Phylogenetic analysis of the ITS sequence, the rbcL gene, and the tufA gene reveals that B. insignis is significantly different from B. texensis, in that it has oil droplets, smaller vegetative cells and zoospores, and distinct habitats. It is also different from B.oleifera as it has smaller vegetative cells and zoospores, turns red after cultivation, has longer flagella, and resides in different habitats. The chloroplast genomes of B. texensis and B. insignis further show significant differences, with the phylogenetic tree constructed based on the analysis of 49 protein-coding genes forming two separate branches. The collinearity of the chloroplast genomes in B. texensis and B. insignis is poor, with 15 out of the 31 homologous modules displaying inversions and complex rearrangements. Given these differences, we classify this alga as a new species and named it Borodinellopsis insignis sp. nov. Full article

Background: Phanera Lour., a genus in the subfamily Cercidoideae of the family Leguminosae, is characterized by woody liana habit, tendrils, and distinctive bilobate or bifoliolate leaves. The genus holds important medicinal value and constitutes a complex group characterized by morphological diversity and unstable taxonomic boundaries. However, limited information on the chloroplast genomes of this genus currently available constrains our understanding of its species diversity. Hence, it is necessary to obtain more chloroplast genome information to uncover the genetic characteristics of this genus. Methods: We collected and assembled the complete chloroplast genomes of nine representative Phanera plants, including Phanera erythropoda, Phanera vahlii, Phanera aureifolia, Phanera bidentata, Phanera japonica, Phanera saigonensis, Phanera championii, Phanera yunnanensis, and Phanera apertilobata. We then conducted a comparative analysis of these genomes and constructed phylogenetic trees. Results: These species are each characterized by a typical quadripartite structure. A total of 130–135 genes were annotated, and the GC content ranged from 39.25–42.58%. Codon usage analysis indicated that codons encoding alanine were dominant. We found 82–126 simple sequence repeats, along with 5448 dispersed repeats, mostly in the form of forward repeats. Phylogenetic analysis revealed that 16 Phanera species form a well-supported monophyletic group, suggesting a possible monophyletic genus. Furthermore, 10 hypervariable regions were detected for identification and evolutionary studies. Conclusions: We focused on comparing chloroplast genome characteristics among nine Phanera species and conducted phylogenetic analyses, laying the foundation for further phylogenetic research and species identification of Phanera. Full article

Vaccinium bracteatum is a valuable plant used both as food and medicine in China, but low production limits the development of its industry. As such, it is important to develop genetic resources for the high-value species for preservation of wild populations and utilization. The complete chloroplast and nuclear genomes have already been available; however, its mitogenome has not yet been characterized. Here, the V. bracteatum mitogenome was assembled using HiFi reads, and a comparative analysis was conducted. The mitogenome was a circular sequence of 708,384 bp with a GC content of 45.28%, in which 67 genes were annotated, including 36 protein-coding genes, 26 tRNA genes, 3 rRNA genes, and 2 pseudogenes. Overall, 370 dispersed repeats, 161 simple repeats, and 42 tandem repeats were identified, and 360 RNA editing sites were predicted. There was extensive DNA migration among the three genomes. In addition, most of the protein-coding genes underwent purifying selection throughout evolution, and the nucleotide diversity was highly variable. In addition, comparative analysis indicated that the sizes, structures, and gene contents of the mitogenomes differed significantly, but the GC contents and functional genes were relatively conserved among the Ericales species. Mitogenome-based phylogenetic analysis indicated the precise. evolutionary and taxonomic status of V. bracteatum. The complete mitogenome represents the last link of the reference genome of V. bracteatum and lays the foundation for effective utilization and molecular breeding of this plant. Full article

×Leymotrigia bergrothii is a presumed hybrid of Leymus arenarius and Elytrigia repens. This article investigates the hybrid origin and genome composition of this species. These plants are sterile, do not undergo pollination, and do not produce seeds; occasionally, underdeveloped stamens containing abortive pollen grains form in individual spikelets. The karyotype analysis of root meristem cells revealed a diploid chromosome number of 49 in ×L. bergrothii, reported here for the first time. Subsequently, we examined the intragenomic polymorphism of the transcribed spacer ITS1 in several species of Elytrigia, Elymus, Leymus, Hordeum, and Psathyrostachys, and compared the ribotype patterns of these species with those of ×L. bergrothii. It is shown that the St-ribotype variants found in Elytrigia repens and Elytrigia pseudocaesia, as well as the ribotypes of the La family, which dominate in the genome of Leymus arenarius, correspond to major ribotypes in ×L. bergrothii. The ribotypes of the St and La families are present in the nuclear genome of ×L. bergrothii in almost equal proportions. A comparison of intron and exon sequences of the trnL gene in the chloroplast DNA of Leymus arenarius, Elytrigia repens, and ×L. bergrothii showed that this region in ×L. bergrothii is identical or very close to that of Elytrigia repens, suggesting that Elytrigia repens was the cytoplasmic donor to ×L. bergrothii. Thus, our study confirms the hypothesis that this species represents a sterile first-generation hybrid of Leymus arenarius and Elytrigia repens, reproducing vegetatively. Full article

Oxyria (Polygonaceae) is a small genus only comprising two species, Oxyria digyna and O. sinensis. Both species have well-documented usage in Chinese herbal medicine. We sequenced and assembled the complete mitogenomes of these two species and conducted a comparative analysis of the mitogenomes within Polygonaceae. Both O. digyna and O. sinensis displayed distinctive multi-branched conformations, consisting of one linear and one circular molecule. These two species shared similar gene compositions and exhibited distinct codon preferences, with mononucleotides as the most abundant type of simple sequence repeats. In the mitogenome of O. sinensis, a pair of long forward repeat sequences can mediate the division of molecule 1 into two sub-genomic circular molecules. Homologous sequence analysis revealed the occurrence of gene transfer between the chloroplast and mitochondrial genomes within Oxyria species. Additionally, a substantial number of homologous collinear blocks with varied arrangements were observed across different Polygonaceae species. Phylogenetic analysis suggested that mitogenome genes can serve as reliable markers for constructing phylogenetic relationships within Polygonaceae. Comparative analysis of eight species revealed Polygonaceae mitogenomes exhibited variability in gene presence, and most protein-coding genes (PCGs) have undergone negative selection. Overall, our study provided a comprehensive overview of the structural, functional, and evolutionary characteristics of the Polygonaceae mitogenomes. Full article

The TCP gene family encodes plant transcription factors crucial for regulating growth and development. While TCP genes have been identified in various species, they have not been studied in Phoebe bournei (Hemsl.). This study identified 29 TCP genes in the P. bournei genome, categorizing them into Class I (PCF) and Class II (CYC/TB1 and CIN). We conducted analyses on the PbTCP gene at both the protein level (physicochemical properties) and the gene sequence level (subcellular localization, chromosomal distribution, phylogenetic relationships, conserved motifs, and gene structure). Most P. bournei TCP genes are localized in the nucleus, except PbTCP9 in the mitochondria and PbTCP8 in both the chloroplast and nucleus. Chromosomal mapping showed 29 TCP genes unevenly distributed across 10 chromosomes, except chromosome 8 and 9. We also analyzed the promoter cis-regulatory elements, which are mainly involved in plant growth and development and hormone responses. Notably, most PbTCP transcription factors respond highly to light. Further analysis revealed three subfamily genes expressed in five P. bournei tissues: leaves, root bark, root xylem, stem xylem, and stem bark, with predominant PCF genes. Using qRT-PCR, we examined six representative genes—PbTCP16, PbTCP23, PbTCP7, PbTCP29, PbTCP14, and PbTCP15—under stress conditions such as high temperature, drought, light exposure, and dark. PbTCP14 and PbTCP15 showed significantly higher expression under heat, drought, light and dark stress. We hypothesize that TCP transcription factors play a key role in growth under varying light conditions, possibly mediated by auxin hormones. This work provides insights into the TCP gene family’s functional characteristics and stress resistance regulation in P. bournei. Full article

Background: Astilbe, consisting of about 18 species, is distributed throughout East Asia and Northeastern America, and most Astilbe species are widely cultivated as ornamental plants. A total of four species of Astilbe have been confirmed to be distributed throughout Korea, two of which are endemic to Korea. Methods: In this study, we sequenced and assembled the complete chloroplast genomes of two endemic Korean plants using Illumina sequencing technology, identified simple sequence repeats (SSRs) and repetitive sequences, and compared them with three previously reported chloroplast genomes. Results: The chloroplast genomes of the two species were 156,968 and 57,142 bp in length and had a four-part circular structure. They consisted of a large single-copy region of 87,223 and 87,272 bp and a small single-copy region of 18,167 and 18,138 bp, separated by a pair of inverted repeats (IRa and IRb, 25,789 and 25,866 bp). The genomes contained 130 genes, 49 SSRs, and 49 long repetitive sequences. Comparative analysis with the chloroplast genomes of five Astilbe species indicated that A. uljinensis was closely related to A. chinensis and A. taquetii to A. koreana. Conclusions: This study provides valuable references for the identification of two endemic Korean Astilbe species and contributes to a deeper understanding of the phylogeny and evolution of the genus Astilbe. Full article

The plasticity elongation of mesocotyl (MES) and coleoptile (COL) largely determines the morphology of maize seedlings under abiotic stresses. The profilin (PRF) proteins play a pivotal role in cytoskeleton dynamics and plant development via regulating actin polymerization. However, little is known about whether and how the expression of the ZmPRF gene family regulates MES and COL elongation in maize under adverse abiotic stresses. Here, a total of eight ZmPRF gene members were identified in the maize genome. They were mainly located in the cytoplasm, chloroplast, and mitochondrion, and clearly divided into four classes, based on phylogenetic analysis. Segmental duplication was the main driver for the expansion of ZmPRF genes. Ka/Ks analysis indicated that most ZmPRF genes were intensely purified and selected. Promoter cis-element analysis suggested their potential roles in response to growth and development, stress adaption, hormone response, and light response. The protein–protein interaction network and two independent RNA-sequencing analyses revealed that eight ZmPRF genes and their thirty-seven interacting genes showed varied expression patterns in MES and COL of three maize genotypes under different sowing depths, 24-epibrassinolide application, and light spectral-quality treatments, of which ZmPRF3.3 was a potential core conserved gene for breeding application. Moreover, the quantitative real-time PCR (qRT-PCR) verified that the relative expression levels of most ZmPRF genes in MES and COL under above treatments were significantly correlated with the plasticity elongation of MES and COL in maize. Therefore, these results perform a comprehensive overview of the ZmPRF family and will provide valuable information for the validation of the function of ZmPRF genes in maize development under diverse abiotic stress. Full article

Background/Objectives: Crassula aquatica (L.) Schonl. is a very small annual plant growing along riverbanks. Chloroplast (cp) genomes, crucial for photosynthesis, are highly conserved and play a key role in understanding plant evolution. In this study, we conducted cp genome analysis of C. aquatica, aiming to elucidate its phylogenetic position and structural variations. We analyzed and described the features of the complete cp genome of C. aquatica and conducted comparative analysis with the cp genomes of closely related taxa. Rsults: The cp genome was 144,503 bp in length and exhibited the typical quadripartite structure, consisting of a large single-copy region (LSC; 77,993 bp), a small single-copy region (SSC; 16,784 bp), and two inverted repeats (24,863 bp). The cp genome of C. aquatica comprised 113 unique genes, including 79 protein-coding genes (PCGs), 30 tRNAs, and 4 rRNA genes. Comparative genomic analysis of 13 other Crassula species and six outgroups demonstrated highly conserved gene content and order among Crassula species. However, notable differences were observed, including the complete loss of the rpoC1 intron in C. aquatica and several closely related species, which may serve as a synapomorphic trait supporting the monophyly of the subgenus Disporocarpa. We analyzed the nucleotide diversity among 14 Crassula cp genomes and identified five highly variable regions (pi > 0.08) in the IGS regions. Phylogenetic analysis based on 78 PCGs confirmed the monophyly of Crassula and its division into two subgenera: Crassula and Disporocarpa. Although the phylogenetic tree supported the subgeneric classification system, the sectional classification system requires reassessment. Conclusions: In this study, we conducted a comparative analysis of the cp genome of the genus Crassula. We inferred evolutionary trends within the Crassula cp genome and provided molecular evidence supporting the integration of the genus Tillaea into the genus Crassula. However, as this study does not represent all species within the genus Tillaea, further comprehensive phylogenetic analyses are requrired. Full article

Gastrodia elata rhizomes have been applied as traditional medicinal materials for thousands of years. In China, G. elata f. elata (red flower and stem, Ge), G. elata f. viridis (green, Gv), and G. elata f. glauca (black, Gg) represent the primary cultivars in artificial cultivation. Although the annual output of G. elata amounts to 150,000 tons, only 20% is Gg. The long production period, low yield, and high quality of Gg led to its extremely high market prices. However, an effective method to identify this crude drug based solely on its morphological or chemical characteristics is lacking. In this study, the complete chloroplast genomes of three G. elata variants were sequenced using the Illumina HiSeq 2500 platform. Another 21 chloroplast genomes from Gastrodia species, which have published in previous reports, were combined and analyzed together. Our results showed that larger genomic sizes, fewer long tandem repeats, and more simple sequence repeats were the major features of the Gg chloroplast genomes. Phylogenetic analysis showed that the Gg samples were separately clustered in a subclade. Moreover, an accession-specific marker was successfully developed and validated for distinguishing additional rhizome samples. Our study provides investigations of the taxonomic relationships of Gastrodia species. The molecular marker will be useful for differentiating Gastrodia products on the market. Full article

Pinus kesiya var. langbianensis, a species endemic to Yunnan, China, accounts for over 90% of Yunnan’s Pinus resin production. However, there is significant variation in resin yield among individuals, and molecular markers for identifying high-yielding individuals have yet to be developed. In this study, a comparative analysis of complete chloroplast genomes of P. kesiya var. langbianensis was conducted to perform a phylogenetic analysis and differentiate high-yielding individuals. Both high-yielding (HY) and low-yielding (LY) trees possess a typical quadripartite structure, with respective genome sizes of 119,812 bp and 119,780 bp. Each chloroplast genome contains 112 genes, including 72 protein-coding genes, 36 tRNAs, and 4 rRNAs. Furthermore, HY and LY trees contain 30 and 34 SSRs, respectively, with mononucleotide repeats being predominant; neither genome exhibited trinucleotide or pentanucleotide repeats. Six highly variable regions were identified: trnI-CAU-psbA, trnH-GUG-trnI-CAU, rpl16, rrn4.5-rrn5, petG-petL, and psaJ. Phylogenetic analysis based on 72 Pinus species revealed that HY and LY trees clustered separately, with the HY tree grouping with P. kesiya and the LY tree with P. yunnanensis. This study provides a theoretical foundation for the molecular identification of high-yield P. kesiya var. langbianensis individuals and enriches the understanding of its phylogenetic relationships. Full article

Hybridization is considered an important mode of species evolution, but the genetic evolutionary process of Anthurium andraeanum hybridization is still poorly characterized. In order to provide the molecular and morphological basis for phylogenetic analysis in A. andraeanum hybridization, we analyzed the morphological, nuclear genomic, and chloroplast genomic data of five A. andraeanum cultivars and explored the correlations between different traits and nuclear and chloroplast genome characteristics. A. andraeanum hybrid 1 is an A. andraeanum ‘Baron’ (♀) × A. andraeanum ‘Spice’ (♂) cross, and A. andraeanum hybrid 2 is an A. andraeanum ‘Cheers’ (♀) × A. andraeanum hybrid 1 (♂) cross. The A. andraeanum hybrids reflected their parents’ heterozygous features in their morphologies, nuclear genomes, and chloroplast genomes. The morphological traits in the F1 generation were widely separated, showing continuous variation. Based on cluster analysis, the five A. andraeanum cultivars could be divided into two groups. The ISSR analysis results were highly correlated with the spathe color. Among the five A. andraeanum cultivars, the composition and structure features of chloroplast genomes were completely the same or highly similar, respectively. Phylogenetic analysis based on complete chloroplast genome data showed that the genetic stability of the chloroplast is high in A. andraeanum, manifested as uniparental maternal inheritance, where the chloroplast genome composition and structural features of hybrids are highly similar to those of the maternal parent. Full article

Gaillardia pulchella is an important plant species with pharmacological and ornamental applications. It contains a wide array of phytocompounds which play roles against diseases. In vitro propagation requires callogenesis and differentiation of plant organs, which offers a sustainable, alternative synthesis of compounds. The morphogenetic processes and the underlying mechanisms are, however, known to be under genetic regulation and are little understood. The present study investigated these events by generating transcriptome data, with de novo assembly of sequences to describe shoot morphogenesis molecularly in G. pulchella. The RNA was extracted from the callus of pre- and post-shoot organogenesis time. The callus induction was optimal using leaf segments cultured onto MS medium containing α-naphthalene acetic acid (NAA; 2.0 mg/L) and 6-benzylaminopurine (BAP; 0.5 mg/L) and further exhibited a high shoot regeneration/caulogenesis ability. A total of 68,366 coding sequences were obtained using Illumina150bpPE sequencing and transcriptome assembly. Differences in gene expression patterns were noted in the studied samples, showing opposite morphogenetic responses. Out of 10,108 genes, 5374 (53%) were downregulated, and there were 4734 upregulated genes, representing 47% of the total genes. Through the heatmap, the top 100 up- and downregulating genes’ names were identified and presented. The up- and downregulated genes were identified using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Important pathways, operative during G. pulchella shoot organogenesis, were signal transduction (13.55%), carbohydrate metabolism (8.68%), amino acid metabolism (5.11%), lipid metabolism (3.75%), and energy metabolism (3.39%). The synthesized proteins displayed phosphorylation, defense response, translation, regulation of DNA-templated transcription, carbohydrate metabolic processes, and methylation activities. The genes’ product also exhibited ATP binding, DNA binding, metal ion binding, protein serine/threonine kinase -, ATP hydrolysis activity, RNA binding, protein kinase, heme and GTP binding, and DNA binding transcription factor activity. The most abundant proteins were located in the membrane, nucleus, cytoplasm, ribosome, ribonucleoprotein complex, chloroplast, endoplasmic reticulum membrane, mitochondrion, nucleosome, Golgi membrane, and other organellar membranes. These findings provide information for the concept of molecular triggers, regulating programming, differentiation and reprogramming of cells, and their uses. Full article

Gentiana rigescens, an alpine plant with significant medicinal value, possesses a complex genetic background. However, comprehensive genomic research on G. rigescens is still lacking, particularly concerning its organelle genome. In this study, G. rigescens was studied to sequence the mitochondrial genome (mitogenome) and ascertain the assembly, informational content, and developmental expression of the mitogenome. The mitogenome of G. rigescens was 393,595 bp in length and comprised four circular chromosomes ranging in size from 6646 bp to 362,358 bp. The GC content was 43.73%. The mitogenome featured 30 distinct protein-coding genes, 26 tRNA genes, and 3 rRNA genes. The mitogenome of G. rigescens also revealed 70 SSRs, which were mostly tetra-nucleotides. In addition, 48 homologous fragments were found between the mitogenome and the chloroplast genome, with the longest measuring 23,330 bp. The documentation of the mitochondrial genome of G. rigescens is instrumental in advancing the understanding of its physiological development. Decoding the G. rigescens mitogenome will offer valuable genetic material for phylogenetic research on Gentianaceae and enhance the use of species germplasm resources. Full article

Orchidantha chinensis T. L. Wu, an endemic species in China, is listed as a key protected wild plant in Guangdong Province. However, the lack of reports on the chloroplast genome and simple sequence repeat (SSR) markers has hindered the assessment of its genetic diversity and conservation strategies. The limited number of molecular markers to assess the genetic diversity of this species, and thus develop proper conservation strategies, highlighted the urgent need to develop new ones. This study developed new SSR markers and investigated genetic variation using 96 samples of O. chinensis from seven populations. Through high-throughput sequencing, a complete chloroplast genome of 134,407 bp was assembled. A maximum-likelihood phylogenetic tree, based on the chloroplast genome, showed that O. chinensis is closely related to Ravenala madagascariensis. The study identified 52 chloroplast SSRs (cpSSRs) and 5094 expressed sequence tag SSRs (EST-SSRs) loci from the chloroplast genome and leaf transcriptome, respectively. Twenty-one polymorphic SSRs (seven cpSSRs and fourteen EST-SSRs) were selected to evaluate the genetic variation in 96 accessions across seven populations. Among these markers, one cpSSR and 11 EST-SSRs had high polymorphism information content (>0.5). Cluster, principal coordinate, and genetic structure analyses indicated that groups G1 and G6 were distinct from the other five groups. However, an analysis of molecular variance showed greater variation within groups than among groups. The genetic distance among the populations was significantly positively correlated with geographical distance. These findings provide new markers for studying the genetic variability of O. chinensis and offer a theoretical foundation for its conservation strategies. Full article