Metagenomic and whole-genome analysis reveals new lineages of gokushoviruses and biogeographic separation in the sea
Much remains to be learned about single-stranded (ss) DNA viruses in natural systems, and the evolutionary relationships among them. One of the eight recognized families of ssDNA viruses is the Microviridae, a group of viruses infecting bacteria. In this study we used metagenomic analysis, genome as...
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ftdatacite:10.6084/m9.figshare.899771.v1 2023-05-15T15:10:26+02:00 Metagenomic and whole-genome analysis reveals new lineages of gokushoviruses and biogeographic separation in the sea Suttle, Curtis Labonté, Jessica 2014 https://dx.doi.org/10.6084/m9.figshare.899771.v1 https://figshare.com/articles/journal_contribution/Metagenomic_and_whole_genome_analysis_reveals_new_lineages_of_gokushoviruses_and_biogeographic_separation_in_the_sea/899771/1 unknown figshare https://dx.doi.org/10.6084/m9.figshare.899771 Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 CC-BY Microbiology FOS Biological sciences 60506 Virology 60102 Bioinformatics FOS Computer and information sciences Marine Biology Oceanography FOS Earth and related environmental sciences Evolutionary Biology Text article-journal Journal contribution ScholarlyArticle 2014 ftdatacite https://doi.org/10.6084/m9.figshare.899771.v1 https://doi.org/10.6084/m9.figshare.899771 2021-11-05T12:55:41Z Much remains to be learned about single-stranded (ss) DNA viruses in natural systems, and the evolutionary relationships among them. One of the eight recognized families of ssDNA viruses is the Microviridae, a group of viruses infecting bacteria. In this study we used metagenomic analysis, genome assembly, and amplicon sequencing of purified ssDNA to show that bacteriophages belonging to the subfamily Gokushovirinae within the Microviridae are genetically diverse and widespread members of marine microbial communities. Metagenomic analysis of coastal samples from the Gulf of Mexico (GOM) and British Columbia, Canada, revealed numerous sequences belonging to gokushoviruses and allowed the assembly of five putative genomes with an organization similar to chlamydiamicroviruses. Fragment recruitment to these genomes from different metagenomic data sets is consistent with gokushovirus genotypes being restricted to specific oceanic regions. Conservation among the assembled genomes allowed the design of degenerate primers that target an 800 bp fragment from the gene encoding the major capsid protein. Sequences could be amplified from coastal temperate and subtropical waters, but not from samples collected from the Arctic Ocean, or freshwater lakes. Phylogenetic analysis revealed that most sequences were distantly related to those from cultured representatives. Moreover, the sequences fell into at least seven distinct evolutionary groups, most of which were represented by one of the assembled metagenomes. Our results greatly expand the known sequence space for gokushoviruses, and reveal biogeographic separation and new evolutionary lineages of gokushoviruses in the oceans Text Arctic Arctic Ocean DataCite Metadata Store (German National Library of Science and Technology) Arctic Arctic Ocean Canada British Columbia ENVELOPE(-125.003,-125.003,54.000,54.000) |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
unknown |
topic |
Microbiology FOS Biological sciences 60506 Virology 60102 Bioinformatics FOS Computer and information sciences Marine Biology Oceanography FOS Earth and related environmental sciences Evolutionary Biology |
spellingShingle |
Microbiology FOS Biological sciences 60506 Virology 60102 Bioinformatics FOS Computer and information sciences Marine Biology Oceanography FOS Earth and related environmental sciences Evolutionary Biology Suttle, Curtis Labonté, Jessica Metagenomic and whole-genome analysis reveals new lineages of gokushoviruses and biogeographic separation in the sea |
topic_facet |
Microbiology FOS Biological sciences 60506 Virology 60102 Bioinformatics FOS Computer and information sciences Marine Biology Oceanography FOS Earth and related environmental sciences Evolutionary Biology |
description |
Much remains to be learned about single-stranded (ss) DNA viruses in natural systems, and the evolutionary relationships among them. One of the eight recognized families of ssDNA viruses is the Microviridae, a group of viruses infecting bacteria. In this study we used metagenomic analysis, genome assembly, and amplicon sequencing of purified ssDNA to show that bacteriophages belonging to the subfamily Gokushovirinae within the Microviridae are genetically diverse and widespread members of marine microbial communities. Metagenomic analysis of coastal samples from the Gulf of Mexico (GOM) and British Columbia, Canada, revealed numerous sequences belonging to gokushoviruses and allowed the assembly of five putative genomes with an organization similar to chlamydiamicroviruses. Fragment recruitment to these genomes from different metagenomic data sets is consistent with gokushovirus genotypes being restricted to specific oceanic regions. Conservation among the assembled genomes allowed the design of degenerate primers that target an 800 bp fragment from the gene encoding the major capsid protein. Sequences could be amplified from coastal temperate and subtropical waters, but not from samples collected from the Arctic Ocean, or freshwater lakes. Phylogenetic analysis revealed that most sequences were distantly related to those from cultured representatives. Moreover, the sequences fell into at least seven distinct evolutionary groups, most of which were represented by one of the assembled metagenomes. Our results greatly expand the known sequence space for gokushoviruses, and reveal biogeographic separation and new evolutionary lineages of gokushoviruses in the oceans |
format |
Text |
author |
Suttle, Curtis Labonté, Jessica |
author_facet |
Suttle, Curtis Labonté, Jessica |
author_sort |
Suttle, Curtis |
title |
Metagenomic and whole-genome analysis reveals new lineages of gokushoviruses and biogeographic separation in the sea |
title_short |
Metagenomic and whole-genome analysis reveals new lineages of gokushoviruses and biogeographic separation in the sea |
title_full |
Metagenomic and whole-genome analysis reveals new lineages of gokushoviruses and biogeographic separation in the sea |
title_fullStr |
Metagenomic and whole-genome analysis reveals new lineages of gokushoviruses and biogeographic separation in the sea |
title_full_unstemmed |
Metagenomic and whole-genome analysis reveals new lineages of gokushoviruses and biogeographic separation in the sea |
title_sort |
metagenomic and whole-genome analysis reveals new lineages of gokushoviruses and biogeographic separation in the sea |
publisher |
figshare |
publishDate |
2014 |
url |
https://dx.doi.org/10.6084/m9.figshare.899771.v1 https://figshare.com/articles/journal_contribution/Metagenomic_and_whole_genome_analysis_reveals_new_lineages_of_gokushoviruses_and_biogeographic_separation_in_the_sea/899771/1 |
long_lat |
ENVELOPE(-125.003,-125.003,54.000,54.000) |
geographic |
Arctic Arctic Ocean Canada British Columbia |
geographic_facet |
Arctic Arctic Ocean Canada British Columbia |
genre |
Arctic Arctic Ocean |
genre_facet |
Arctic Arctic Ocean |
op_relation |
https://dx.doi.org/10.6084/m9.figshare.899771 |
op_rights |
Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.6084/m9.figshare.899771.v1 https://doi.org/10.6084/m9.figshare.899771 |
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1766341468767649792 |