Phylogenomic analysis expands the known repertoire of single-stranded DNA viruses in benthic zones of the South Indian Ocean

dc.contributor.authorBezuidt, Keoagile Ignatius Oliver
dc.contributor.authorMakhalanyane, Thulani Peter
dc.date.accessioned2024-11-05T09:26:07Z
dc.date.available2024-11-05T09:26:07Z
dc.date.issued2024-01
dc.descriptionDATA AVAILABILITY: Raw sequence data linked to study have been deposited to the NCBI SRA under accession number PRJNA894371. Supplemental materials are available on the following link: https://doi.org/10.6084/m9.figshare.24032697.en_US
dc.descriptionSUPPLEMENTARY TABLES : SUPPLEMENTARY TABLE S1: Physical and chemical properties of the deep ocean samples 3 from the South Indian Ocean sampling sites. SUPPLEMENTARY TABLE S2: Output summary of results from CheckV. The table indicates the quality scores for viruses predicted using the VirFinder pipeline. SUPPLEMENTARY TABLE S3: Output summary of results from CheckV. The table shows the quality estimates of the putative viruses predicted using the VirSorter2 pipeline. SUPPLEMENTARY TABLE S4: A table indicating the IDs of various KOs associated with the 85 putative AMGs detected in dsDNA viruses from the SIO. SUPPLEMENTARY TABLE S5: A list of pathways predicted to be associated with the KOs and putative AMGs detected in dsDNA viruses from the SIO. SUPPLEMENTARY TABLE S6: Blastp verification of putative ssDNA viruses predicted using VirSorter2 pipeline. SUPPLEMENTARY TABLE S7: Blastp and HHpred verification of putative Cressdnaviricota-associated Rep proteins predicted using our HMM-based approach. SUPPLEMENTARY TABLE 8: Blastp verification of putative Phixviricota-associated VP1 proteins predicted using our HMM-based approach.en_US
dc.descriptionSUPPLEMENTARY FIGURES : SUPPLEMENTARY FIGURE S1 Summary statistics for our metagenomic data. The curves together with the dashed red lines show that our metagenomes had estimated coverage >95%. SUPPLEMENTARY FIGURE S2 Bar plots indicating the distribution of Eukaryota associated with the metagenomic dataset. SUPPLEMENTARY FIGURE S3 Sequence similarity networks generated using 1e-60 showing Major Capsid protein sequences acquired from this study and NCBI GenBank. SUPPLEMENTARY FIGURE S4 Sequence similarity networks of genes acquired from “dark matter” associated circular genetic elements (viral) contigs. Clusters are assigned colours based on structural predictions derived from HHpred. Clusters with >85% probability scores are indicated by different colors that distinguishes them from hypothetical proteins.en_US
dc.description.abstractSingle-stranded (ss) DNA viruses are ubiquitous and constitute some of the most diverse entities on Earth. Most studies have focused on ssDNA viruses from terrestrial environments resulting in a significant deficit in benthic ecosystems including aphotic zones of the South Indian Ocean (SIO). Here, we assess the diversity and phylogeny of ssDNA in deep waters of the SIO using a combination of established viral taxonomy tools and a Hidden Markov Model based approach. Replication initiator protein-associated (Rep) phylogenetic reconstruction and sequence similarity networks were used to show that the SIO hosts divergent and as yet unknown circular Rep-encoding ssDNA viruses. Several sequences appear to represent entirely novel families, expanding the repertoire of known ssDNA viruses. Results suggest that a small proportion of these viruses may be circular genetic elements, which may strongly influence the diversity of both eukaryotes and prokaryotes in the SIO. Taken together, our data show that the SIO harbours a diverse assortment of previously unknown ssDNA viruses. Due to their potential to infect a variety of hosts, these viruses may be crucial for marine nutrient recycling through their influence of the biological carbon pump.en_US
dc.description.departmentBiochemistry, Genetics and Microbiology (BGM)en_US
dc.description.librarianhj2024en_US
dc.description.sdgSDG-14:Life below wateren_US
dc.description.sponsorshipThe National Research Foundation of South Africa and the South African National Antarctic Program. The Technology Innovation Agency supported the sequencing costs. The project also received funding from the European Union’s Horizon 2020 research and innovation programme as part of the AtlantECO project.en_US
dc.description.urihttps://academic.oup.com/ismecommunen_US
dc.identifier.citationOliver, K. I. Bezuidt, Thulani P. Makhalanyane, Phylogenomic analysis expands the known repertoire of single-stranded DNA viruses in benthic zones of the South Indian Ocean, ISME Communications, Volume 4, Issue 1, January 2024, ycae065, https://doi.org/10.1093/ismeco/ycae065.en_US
dc.identifier.issn2730-6151 (online)
dc.identifier.other10.1093/ismeco/ycae065
dc.identifier.urihttp://hdl.handle.net/2263/98926
dc.language.isoenen_US
dc.publisherOxford University Pressen_US
dc.rights© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology. This is an open access article distributed under the terms of the Creative Commons CC BY license.en_US
dc.subjectBiogeochemical cyclingen_US
dc.subjectCRESS-DNAen_US
dc.subjectDeoxyribonucleic acid (DNA)en_US
dc.subjectSingle stranded DNA virusesen_US
dc.subjectRep and Capsid proteinsen_US
dc.subjectSouth Indian Ocean (SIO)en_US
dc.subjectViral diversityen_US
dc.subjectSDG-14: Life below wateren_US
dc.titlePhylogenomic analysis expands the known repertoire of single-stranded DNA viruses in benthic zones of the South Indian Oceanen_US
dc.typeArticleen_US

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