Functional Profiling and Evolutionary Analysis of a Marine Microalgal Virus Pangenome
<p>Phylogeny, geographical origin, and pangenome density of available Coccolithovirus genomes: (<b>A</b>) The phylogeny displayed here is a midpoint-rooted cladogram created with RAxML (GTRGAMMA) from the panX alignment data. The phylogeny with branch lengths displayed is in <a href="#app1-viruses-15-01116" class="html-app">Figure S1</a>. CDS numbers are from NCBI GenBank files and are slightly different than previously reported numbers in Nissimov et al. [<a href="#B12-viruses-15-01116" class="html-bibr">12</a>] from an alternate pipeline. (<b>B</b>) Approximate sampling locations around the coast of Great Britain and Norway. For exact GPS coordinates and depth, see <a href="#app1-viruses-15-01116" class="html-app">Table S1</a>. (<b>C</b>) Gene distribution across the 14 Coccolithovirus genomes, with the number of genes found in each genome. An aligned relative density estimate of the histogram is displayed on the alternative <span class="html-italic">y</span>-axis (right). The darker column represents genes that were shared across every Coccolithovirus strain in the pangenome. Re-annotated Coccolithoviruses (using Prokka) were also used to create a pangenome (displayed in <a href="#app1-viruses-15-01116" class="html-app">Figure S2</a>) with a very similar distribution (core genes changing from 30.25% to 34.50% of the pangenome).</p> "> Figure 2
<p>Genome comparison of Coccolithoviruses using EhV-86 as a representative. NC_007346 was used as the query against all Coccolithovirus genomes. The percent alignment identity across regions of EhV-86 to other Coccolithovirus strains is indicated based on colour intensity. Rings (EhV strains) are coloured and grouped by subclade. The black bar indicates a long region of interest with predominantly core genes. Generated with BLAST Ring Image Generator (BRIG) v0.95 [<a href="#B41-viruses-15-01116" class="html-bibr">41</a>]. This alignment shows the genetic content in the pangenome in relation to EhV-86. The genomes have different lengths and different numbers of genes (see <a href="#app1-viruses-15-01116" class="html-app">Table S1</a>). For an overview of the pangenome gene presence/absence, see <a href="#app1-viruses-15-01116" class="html-app">Figure S2</a>.</p> "> Figure 3
<p>Annotation coverage and AlphaFold results for EhV-86: (<b>A</b>) All 12 annotation sources collected and/or generated for EhV-86. Any proteins called “hypothetical protein”, “putative membrane protein”, “uncharacterized protein”, or (in the case of EggNOG) not having any free text description were not included as “annotated”. Combined indicates all proteins with at least one annotation in any of the other categories. The Ku et al. [<a href="#B16-viruses-15-01116" class="html-bibr">16</a>] annotation set is a manual curation of EhV-201 annotations from other papers as well as BLAST searches against a variety of databases. The PDB (remote homology) annotations were retrieved from Mirzakhanyan and Gershon [<a href="#B28-viruses-15-01116" class="html-bibr">28</a>]. These data are included in <a href="#app1-viruses-15-01116" class="html-app">Table S4</a>. (<b>B</b>) Frequency of COG categories in Coccolithoviruses, divided into the core and accessory pangenome. Frequency here is the number of genes with the COG category in a genome. Counts less than 3 are not labelled. COG annotations derive from the EggNOG annotation database using emapper v2.0.1b. This method, likely due to genetic differences, does not always annotate every gene clustered together by panX in the same way (meaning that core genes do not always have equal counts of functorial categories across the figure). (<b>C</b>) The chain pLDDT scores for the best scoring model AlphaFold predicted for EhV-86 proteins. Chain pLDDT (predicted local distance difference test) scores closer to 100 show greater overall model confidence, being an average of the per-residue pLDDT values across the entire predicted structure.</p> "> Figure 4
<p>The majority taxonomy from EhV-86 BLASTP hits divided into different alignment percent identity ranges. The denominator for the percentages on the <span class="html-italic">x</span>-axis is indicated on the <span class="html-italic">y</span>-axis after the pangenome category (i.e., Core (240)). This is the number of EhV-86 proteins that had a majority taxonomy for that alignment percent identity range. The taxonomy in the legend is indented to indicate the taxonomic level. Only taxa present at greater than two percent within their category (<span class="html-italic">y</span>-axis) are displayed here. A full table of these data is available in <a href="#app1-viruses-15-01116" class="html-app">Table S7</a>.</p> "> Figure 5
<p>EhV-201 expression data from Ku et al. (2020) [<a href="#B16-viruses-15-01116" class="html-bibr">16</a>] broken up into core and accessory genes based on the pangenome analysis. The infection phase categories on the <span class="html-italic">x</span>-axis are from a hierarchical clustering analysis (MetaCell method using the k-nearest neighbor graph partitions) of the expression data performed by Ku et al. [<a href="#B16-viruses-15-01116" class="html-bibr">16</a>] looking at a 0–24 h post-infection time range of <span class="html-italic">E. huxleyi</span> CCMP2090 infected by EhV-201.</p> ">
Abstract
:1. Introduction
2. Materials and Methods
2.1. Pangenome Analysis of the Genus Coccolithovirus and Comparison to Chloroviruses and Prasinoviruses
2.2. Expanding the Coccolithovirus Annotation Profile
2.3. Taxonomy Distribution of EhV-86 Protein Homologs
2.4. Transcriptome Analysis
3. Results and Discussion
3.1. The Coccolithovirus Pangenome
3.2. Expanding the Coccolithovirus Functional Profile
3.3. Taxonomy Distribution of EhV-86 Protein Homologues
3.4. Pangenome Expression Profile
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Coccolithovirus Pangenome | Common Domain/Protein Family/Structural Matches for Non-Annotated Proteins | Number of Sources with Similar Hits | Sources with Similar Hits | |
---|---|---|---|---|
ehv116 | accessory (12 strains) | Fatty acid hydroxylase | 8 | InterPro, Pfam, PDB, Phyre2, EggNOG, Uniclust, Ku et al. [16], Foldseek |
ehv138 | accessory (12 strains) | Recombination endonuclease VII domain-containing protein | 8 | InterPro, PFAM, PDB, Phyre2, EggNOG, panX, Ku et al. [16], Foldseek |
ehv088 | accessory (12 strains) | Fatty acid hydroxylase | 7 | InterPro, Pfam, PDB, Phyre2, EggNOG, Uniclust, Foldseek |
ehv411 | core | Glycosyltransferase (GlcNAc) | 7 | InterPro, Pfam, PDB, EggNOG, Uniclust, Ku et al. [16], Foldseek |
ehv452 | core | HMG-box domain-containing protein (Uniclust annotated as signal recognition particle-docking protein FtsY) | 7 | InterPro, Pfam, PDB, Phyre2, EggNOG* (Chromatin structure and dynamics: DNA binding, bending), panX, Foldseek |
ehv001 | accessory (5 strains) | Recombination endonuclease VII domain-containing protein | 6 | InterPro, Pfam, PDB, Phyre2, Uniclust, Foldseek |
ehv091 | accessory (12 strains) | Zinc finger, C3HC4 RING-type | 6 | InterPro, Pfam, PDB, Phyre2, Uniclust, Foldseek |
ehv403 | core | Poxvirus VLTF3 | 6 | InterPro, Pfam, EggNOG, Uniclust, Ku et al. [16], Foldseek |
ehv463 | accessory (9 strains) | NFACT protein RNA-binding domain-containing protein (can show up in fibronectin-/fibrinogen-binding proteins by similarity) | 6 | Pfam, PDB, Uniclust, panX, Ku et al. [16], Foldseek |
ehv355 | core | Phytanoyl-CoA dioxygenase domain-containing protein (Uniclust annotated as ricin B-type lectin domain-containing protein) | 6 | InterPro, Pfam, PDB, Phyre2, EggNOG* (acid phosphatase activity), Foldseek |
ehv458 | core | RNA polymerase Rpb6 | 6 | InterPro, PDB*(RNA polymerase Rpb8), Phyre2, Uniclust* (DNA-directed RNA polymerase I II), panX, Foldseek |
ehv058 | core | Helicase C-like | 5 | InterPro, Pfam, PDB, EggNOG, Foldseek |
ehv177 | accessory (10 strains) | Zinc finger, RING-type | 5 | InterPro, PDB, Phyre2, Uniclust, Foldseek |
ehv387 | core | Telomere resolvase | 5 | InterPro, Pfam, PDB, Ku et al. [16], Foldseek |
ehv367 | core | SEC-C motif-containing protein | 5 | InterPro, Pfam, PDB, Phyre2* (low alignment coverage), Foldseek |
ehv055 | core | Heliorhodopsin | 5 | InterPro, Pfam, Phyre2, PDB* (rhodopsin), Foldseek |
ehv078 | core | Heliorhodopsin | 5 | InterPro, Pfam, Phyre2, PDB* (rhodopsin), Foldseek |
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Lobb, B.; Shapter, A.; Doxey, A.C.; Nissimov, J.I. Functional Profiling and Evolutionary Analysis of a Marine Microalgal Virus Pangenome. Viruses 2023, 15, 1116. https://doi.org/10.3390/v15051116
Lobb B, Shapter A, Doxey AC, Nissimov JI. Functional Profiling and Evolutionary Analysis of a Marine Microalgal Virus Pangenome. Viruses. 2023; 15(5):1116. https://doi.org/10.3390/v15051116
Chicago/Turabian StyleLobb, Briallen, Anson Shapter, Andrew C. Doxey, and Jozef I. Nissimov. 2023. "Functional Profiling and Evolutionary Analysis of a Marine Microalgal Virus Pangenome" Viruses 15, no. 5: 1116. https://doi.org/10.3390/v15051116
APA StyleLobb, B., Shapter, A., Doxey, A. C., & Nissimov, J. I. (2023). Functional Profiling and Evolutionary Analysis of a Marine Microalgal Virus Pangenome. Viruses, 15(5), 1116. https://doi.org/10.3390/v15051116