Variation in the Genetic Repertoire of Viruses Infecting Micromonas pusilla Reflects Horizontal Gene Transfer and Links to Their Environmental Distribution
<p>Venn diagram of shared coding sequences (CDS) of four MpVs and <span class="html-italic">M. pusilla</span> UTEX LB991, based on clusters by 0.5 amino acid identity. Dashed circles represent host genes shared with viruses.</p> "> Figure 2
<p>Presumed origin of 90 genes with a functional annotation in the four <span class="html-italic">M. pusilla</span> viruses examined in this study. Numbers indicate the number of genes assigned to putative origins. Origin is based on BLAST-P hits against the nr-database.</p> "> Figure 3
<p>Phylogeny of prasinoviruses infecting the genera <span class="html-italic">Ostreococcus</span> (OtV1, OtV2, OtV5, OtV6, OlV1), <span class="html-italic">Bathyococcus</span> (BpV1, BpV2), <span class="html-italic">Micromonas</span> (MpV1, MpV-12T, MpV-PL1, MpV-SP1), and <span class="html-italic">Chlorella</span> (PBCV1, AR158). The neighbor-joining tree is based on the presence and absence of shared putative genes. Bootstrap values are based on 1000 iterations of sub-sampling.</p> "> Figure 4
<p>Maximum likelihood tree of prasinoviruses and chloroviruses infecting the genera <span class="html-italic">Ostreococcus</span> (OtV1, OtV2, OtV5, OtV6, OlV1), <span class="html-italic">Bathyococcus</span> (BpV1, BpV2), <span class="html-italic">Micromonas</span> (MpV1, MpV-12T, MpV-PL1, MpV-SP1), and <span class="html-italic">Chlorella</span> (PBCV1, AR158). The phylogeny is based on full-length DNA polymerase B (DNApol) sequences, bootstrap values based on 1000 iterations; the scale bar represents the substitution rate.</p> "> Figure 5
<p>Variation in phylogenetic distance based on DNApol. The standard deviation (stdv) of the pairwise phylogenetic distances of full-length DNApol sequences of reference virus clusters are shown against their corresponding amplicon equivalents at different levels of % amino acid (aa) identity to demonstrate that amplicon sequences clustered at 97% identity are representative of the full-length sequences.</p> "> Figure 6
<p>Sampling locations (<b>A</b>) and corresponding environmental parameters, sea surface temperature ((<b>B</b>) SST, °C), photosynthetically-active radiation ((<b>C</b>) PAR, μmol photons m<sup>−2</sup> s<sup>−1</sup>) and Chlorophyll <span class="html-italic">a</span> concentration ((<b>D</b>) Chl, mg m<sup>−3</sup>), all based on 32-day composite data from the Aqua MODIS satellite. Sampling stations: Juan de Fuca Strait (JF), Jericho Pier (JP), Point Atkinson (PA), and Saanich Inlet (SI). lat: Degree latitude; long: Degree longitude.</p> "> Figure 7
<p>Maximum likelihood tree of 197 partial phycodnavirus DNApol sequences from five environmental samples clustered at 97% aa identity. Reference sequences are highlighted in purple, dominant OTUs and branches for the environmental samples are indicated in green for JP, PA, JF, SI. Black branches represent other operational taxonomic units (OTUs). Bootstrap values indicate branch support, values from 50 to 100% are shown as size-dependent circles.</p> ">
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sequencing and Annotation of Micromonas pusilla Viruses
2.2. Comparing Prasinovirus Genomes and Inferring Viral Phylogeny
2.3. Assessing the Prevalence of Prasinoviruses in Environmental Samples
3. Results
3.1. Origin and Distribution of Genes in Micromonas Viruses
3.2. Deriving Similarity in Gene Content from DNApol
3.3. Environmental Prevalence of Prasinoviruses Show Adaptation to Environmental Conditions
4. Discussion
4.1. Origin and Distribution of Genes in Micromonas Viruses
4.2. Deriving Similarity in Gene Content from DNA Polymerase
4.3. Environmental Prevalence of Prasinoviruses Show Adaptation to Environmental Conditions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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MpV-PL1 | MpV-SP1 | MpV1 | MpV-12T | |
---|---|---|---|---|
Genome size (bp) | 196,960 | 173,350 | 184,095 | 205,622 |
Host | MpUTEX991 | MpUTEX991 | MpRCC1109 | MpLAC38 |
# ORF | 275 | 248 | 244 | 253 |
ORF length | 684 | 659 | 715 | 749 |
% GC | 43.3 | 40.6 | 41.0 | 39.8 |
Asn-tRNA | 1 | 1 | 1 | 2 |
Gle-tRNA | 1 | 1 | 1 | 1 |
Ile-tRNA | 1 | 1 | 1 | 1 |
Leu-tRNA | 0 | 1 | 1 | 1 |
Thr-tRNA | 1 | 1 | 1 | 1 |
Tyr-tRNA | 1 | 1 | 1 | 1 |
Core-Genes | Pan-Genes | ||
---|---|---|---|
Class | Putative Function | Class | Putative Function |
DNA replication | DNA polymerase | AA synthesis | Acetolacetate synthase |
DNA topoisomerase | Acetolactate synthase | ||
DNA ligase | Aminotransferase | ||
DNA primase | DNA repair | Heat shock protein 70 | |
Nucleotide metabolism | RNase/ | Site specific DNA methylases/ | |
Ribonuclease | methyltransferases | ||
Ribonucleotide reductase | |||
Transcription | mRNA capping enzyme | Sugar manipulation | dTDP-d-glucose 4,6-dehydratase |
Transcription initiation factor | UDP-glucose 6-dehydrogenase | ||
Transcription elongation factor | 6-phosphofructokinase | ||
Structural genes | Capsid protein | Transketolase N-terminal | |
Major capsid protein | Transketolase B subunit | ||
Metabolism | PhoH | Total Shared | 108 |
Total Core | 119 | Total Unique | 327 |
Presence-Absence (aa id 50%) | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CDS Clusters | MpV1 | MPV-12T | MpV-PL1 | MpV-SP1 | BpV1 | BpV2 | OtV1 | OtV2 | OtV5 | OtV6 | OlV1 | PBCV1 | AR158 | |
DNApol | MpV1 | 244 | 0.98 | 0.64 | 0.66 | 1.11 | 1.08 | 0.63 | 0.72 | 0.69 | 0.57 | 0.68 | 4.99 | 5.40 |
MPV-12T | 0.36 | 252 | 1.02 | 0.99 | 1.18 | 1.16 | 1.06 | 1.05 | 1.11 | 1.00 | 1.06 | 5.41 | 5.01 | |
MpV-PL1 | 0.26 | 0.36 | 271 | 0.30 | 1.12 | 1.10 | 0.71 | 0.75 | 0.75 | 0.67 | 0.73 | 5.04 | 5.45 | |
MpV-SP1 | 0.23 | 0.36 | 0.18 | 244 | 1.09 | 1.10 | 0.70 | 0.75 | 0.77 | 0.69 | 0.71 | 4.99 | 5.40 | |
BpV1 | 0.38 | 0.42 | 0.38 | 0.39 | 202 | 0.24 | 1.07 | 1.16 | 1.17 | 1.15 | 1.13 | 4.89 | 4.90 | |
BpV2 | 0.39 | 0.42 | 0.38 | 0.39 | 0.05 | 209 | 1.05 | 1.17 | 1.13 | 1.11 | 1.13 | 4.91 | 4.92 | |
OtV1 | 0.27 | 0.33 | 0.24 | 0.25 | 0.37 | 0.38 | 230 | 0.29 | 0.25 | 0.42 | 0.24 | 5.36 | 5.37 | |
OtV2 | 0.26 | 0.33 | 0.23 | 0.24 | 0.41 | 0.41 | 0.05 | 235 | 0.33 | 0.48 | 0.22 | 6.07 | 6.08 | |
OtV5 | 0.27 | 0.33 | 0.25 | 0.25 | 0.37 | 0.38 | 0.01 | 0.06 | 260 | 0.46 | 0.28 | 5.42 | 5.43 | |
OtV6 | 0.26 | 0.35 | 0.25 | 0.24 | 0.38 | 0.38 | 0.09 | 0.10 | 0.09 | 249 | 0.45 | 5.40 | 5.41 | |
OlV1 | 0.28 | 0.35 | 0.25 | 0.24 | 0.39 | 0.40 | 0.08 | 0.08 | 0.08 | 0.09 | 246 | 6.09 | 6.10 | |
PBCV1 | 2.09 | 2.15 | 2.19 | 2.05 | 2.03 | 2.05 | 2.21 | 2.21 | 2.22 | 2.13 | 2.16 | 789 | 0.81 | |
AR158 | 2.15 | 2.18 | 2.23 | 2.10 | 2.07 | 2.08 | 2.27 | 2.27 | 2.30 | 2.22 | 2.25 | 0.12 | 806 | |
Mantel Test | 0.96, p = 0.01 | 0.99, p = 0.01 |
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Finke, J.F.; Winget, D.M.; Chan, A.M.; Suttle, C.A. Variation in the Genetic Repertoire of Viruses Infecting Micromonas pusilla Reflects Horizontal Gene Transfer and Links to Their Environmental Distribution. Viruses 2017, 9, 116. https://doi.org/10.3390/v9050116
Finke JF, Winget DM, Chan AM, Suttle CA. Variation in the Genetic Repertoire of Viruses Infecting Micromonas pusilla Reflects Horizontal Gene Transfer and Links to Their Environmental Distribution. Viruses. 2017; 9(5):116. https://doi.org/10.3390/v9050116
Chicago/Turabian StyleFinke, Jan F., Danielle M. Winget, Amy M. Chan, and Curtis A. Suttle. 2017. "Variation in the Genetic Repertoire of Viruses Infecting Micromonas pusilla Reflects Horizontal Gene Transfer and Links to Their Environmental Distribution" Viruses 9, no. 5: 116. https://doi.org/10.3390/v9050116
APA StyleFinke, J. F., Winget, D. M., Chan, A. M., & Suttle, C. A. (2017). Variation in the Genetic Repertoire of Viruses Infecting Micromonas pusilla Reflects Horizontal Gene Transfer and Links to Their Environmental Distribution. Viruses, 9(5), 116. https://doi.org/10.3390/v9050116