HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts
Identifieur interne : 000029 ( Main/Exploration ); précédent : 000028; suivant : 000030HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts
Auteurs : Patrick W. Laffy [Australie] ; Elisha M. Wood-Charlson [États-Unis] ; Dmitrij Turaev [Autriche] ; Karen D. Weynberg [Australie] ; Emmanuelle S. Botté [Australie] ; Madeleine J. H. Van Oppen [Australie] ; Nicole S. Webster [Australie] ; Thomas Rattei [Autriche]Source :
- Frontiers in Microbiology [ 1664-302X ] ; 2016.
Abstract
Abundant bioinformatics resources are available for the study of complex microbial metagenomes, however their utility in viral metagenomics is limited. HoloVir is a robust and flexible data analysis pipeline that provides an optimized and validated workflow for taxonomic and functional characterization of viral metagenomes derived from invertebrate holobionts. Simulated viral metagenomes comprising varying levels of viral diversity and abundance were used to determine the optimal assembly and gene prediction strategy, and multiple sequence assembly methods and gene prediction tools were tested in order to optimize our analysis workflow. HoloVir performs pairwise comparisons of single read and predicted gene datasets against the viral RefSeq database to assign taxonomy and additional comparison to phage-specific and cellular markers is undertaken to support the taxonomic assignments and identify potential cellular contamination. Broad functional classification of the predicted genes is provided by assignment of COG microbial functional category classifications using EggNOG and higher resolution functional analysis is achieved by searching for enrichment of specific Swiss-Prot keywords within the viral metagenome. Application of HoloVir to viral metagenomes from the coral
Url:
DOI: 10.3389/fmicb.2016.00822
PubMed: 27375564
PubMed Central: 4899465
Affiliations:
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Laffy</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Australian Institute of Marine Science</institution><country>Townsville, QLD, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation></author><author><name sortKey="Wood Charlson, Elisha M" sort="Wood Charlson, Elisha M" uniqKey="Wood Charlson E" first="Elisha M." last="Wood-Charlson">Elisha M. Wood-Charlson</name><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Center for Microbial Oceanography: Research and Education, University of Hawai‘i at Mānoa</institution><country>Honolulu, HI, USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation></author><author><name sortKey="Turaev, Dmitrij" sort="Turaev, Dmitrij" uniqKey="Turaev D" first="Dmitrij" last="Turaev">Dmitrij Turaev</name><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna</institution><country>Vienna, Austria</country></nlm:aff><country xml:lang="fr">Autriche</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation></author><author><name sortKey="Weynberg, Karen D" sort="Weynberg, Karen D" uniqKey="Weynberg K" first="Karen D." last="Weynberg">Karen D. Weynberg</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Australian Institute of Marine Science</institution><country>Townsville, QLD, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation></author><author><name sortKey="Botte, Emmanuelle S" sort="Botte, Emmanuelle S" uniqKey="Botte E" first="Emmanuelle S." last="Botté">Emmanuelle S. Botté</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Australian Institute of Marine Science</institution><country>Townsville, QLD, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation></author><author><name sortKey="Van Oppen, Madeleine J H" sort="Van Oppen, Madeleine J H" uniqKey="Van Oppen M" first="Madeleine J. H." last="Van Oppen">Madeleine J. H. Van Oppen</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Australian Institute of Marine Science</institution><country>Townsville, QLD, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff4"><institution>School of Biosciences, University of Melbourne</institution><country>Melbourne, VIC, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation></author><author><name sortKey="Webster, Nicole S" sort="Webster, Nicole S" uniqKey="Webster N" first="Nicole S." last="Webster">Nicole S. Webster</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Australian Institute of Marine Science</institution><country>Townsville, QLD, Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation></author><author><name sortKey="Rattei, Thomas" sort="Rattei, Thomas" uniqKey="Rattei T" first="Thomas" last="Rattei">Thomas Rattei</name><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna</institution><country>Vienna, Austria</country></nlm:aff><country xml:lang="fr">Autriche</country><wicri:regionArea></wicri:regionArea><wicri:regionArea># see nlm:aff region in country</wicri:regionArea></affiliation></author></analytic><series><title level="j">Frontiers in Microbiology</title><idno type="eISSN">1664-302X</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Abundant bioinformatics resources are available for the study of complex microbial metagenomes, however their utility in viral metagenomics is limited. HoloVir is a robust and flexible data analysis pipeline that provides an optimized and validated workflow for taxonomic and functional characterization of viral metagenomes derived from invertebrate holobionts. Simulated viral metagenomes comprising varying levels of viral diversity and abundance were used to determine the optimal assembly and gene prediction strategy, and multiple sequence assembly methods and gene prediction tools were tested in order to optimize our analysis workflow. HoloVir performs pairwise comparisons of single read and predicted gene datasets against the viral RefSeq database to assign taxonomy and additional comparison to phage-specific and cellular markers is undertaken to support the taxonomic assignments and identify potential cellular contamination. Broad functional classification of the predicted genes is provided by assignment of COG microbial functional category classifications using EggNOG and higher resolution functional analysis is achieved by searching for enrichment of specific Swiss-Prot keywords within the viral metagenome. Application of HoloVir to viral metagenomes from the coral <italic>Pocillopora damicornis</italic> and the sponge <italic>Rhopaloeides odorabile</italic> demonstrated that HoloVir provides a valuable tool to characterize holobiont viral communities across species, environments, or experiments.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Abergel, C" uniqKey="Abergel C">C. Abergel</name></author><author><name sortKey="Rudinger Thirion, J" uniqKey="Rudinger Thirion J">J. Rudinger-Thirion</name></author><author><name sortKey="Giege, R" uniqKey="Giege R">R. Giegé</name></author><author><name sortKey="Claverie, J M" uniqKey="Claverie J">J. M. 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Borodovsky</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Australie</li><li>Autriche</li><li>États-Unis</li></country></list><tree><country name="Australie"><noRegion><name sortKey="Laffy, Patrick W" sort="Laffy, Patrick W" uniqKey="Laffy P" first="Patrick W." last="Laffy">Patrick W. Laffy</name></noRegion><name sortKey="Botte, Emmanuelle S" sort="Botte, Emmanuelle S" uniqKey="Botte E" first="Emmanuelle S." last="Botté">Emmanuelle S. Botté</name><name sortKey="Van Oppen, Madeleine J H" sort="Van Oppen, Madeleine J H" uniqKey="Van Oppen M" first="Madeleine J. H." last="Van Oppen">Madeleine J. H. Van Oppen</name><name sortKey="Van Oppen, Madeleine J H" sort="Van Oppen, Madeleine J H" uniqKey="Van Oppen M" first="Madeleine J. H." last="Van Oppen">Madeleine J. H. Van Oppen</name><name sortKey="Webster, Nicole S" sort="Webster, Nicole S" uniqKey="Webster N" first="Nicole S." last="Webster">Nicole S. Webster</name><name sortKey="Weynberg, Karen D" sort="Weynberg, Karen D" uniqKey="Weynberg K" first="Karen D." last="Weynberg">Karen D. Weynberg</name></country><country name="États-Unis"><noRegion><name sortKey="Wood Charlson, Elisha M" sort="Wood Charlson, Elisha M" uniqKey="Wood Charlson E" first="Elisha M." last="Wood-Charlson">Elisha M. Wood-Charlson</name></noRegion></country><country name="Autriche"><noRegion><name sortKey="Turaev, Dmitrij" sort="Turaev, Dmitrij" uniqKey="Turaev D" first="Dmitrij" last="Turaev">Dmitrij Turaev</name></noRegion><name sortKey="Rattei, Thomas" sort="Rattei, Thomas" uniqKey="Rattei T" first="Thomas" last="Rattei">Thomas Rattei</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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