Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages

Handle URI:
http://hdl.handle.net/10754/592606
Title:
Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages
Authors:
Lescot, Magali; Hingamp, Pascal; Kojima, Kenji K; Villar, Emilie; Romac, Sarah; Veluchamy, Alaguraj; Boccara, Martine; Jaillon, Olivier ( 0000-0002-7237-9596 ) ; Ludicone, Daniele ( 0000-0002-7473-394X ) ; Bowler, Chris; Wincker, Patrick; Claverie, Jean-Michel; Ogata, Hiroyuki ( 0000-0001-6594-377X )
Abstract:
Genes encoding reverse transcriptases (RTs) are found in most eukaryotes, often as a component of retrotransposons, as well as in retroviruses and in prokaryotic retroelements. We investigated the abundance, classification and transcriptional status of RTs based on Tara Oceans marine metagenomes and metatranscriptomes encompassing a wide organism size range. Our analyses revealed that RTs predominate large-size fraction metagenomes (>5 μm), where they reached a maximum of 13.5% of the total gene abundance. Metagenomic RTs were widely distributed across the phylogeny of known RTs, but many belonged to previously uncharacterized clades. Metatranscriptomic RTs showed distinct abundance patterns across samples compared with metagenomic RTs. The relative abundances of viral and bacterial RTs among identified RT sequences were higher in metatranscriptomes than in metagenomes and these sequences were detected in all metatranscriptome size fractions. Overall, these observations suggest an active proliferation of various RT-assisted elements, which could be involved in genome evolution or adaptive processes of plankton assemblage.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Center for Desert Agriculture
Citation:
Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages 2015 The ISME Journal
Publisher:
Nature Publishing Group
Journal:
The ISME Journal
Issue Date:
27-Nov-2015
DOI:
10.1038/ismej.2015.192
Type:
Article
ISSN:
1751-7362; 1751-7370
Additional Links:
http://www.nature.com/doifinder/10.1038/ismej.2015.192
Appears in Collections:
Articles; Center for Desert Agriculture; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorLescot, Magalien
dc.contributor.authorHingamp, Pascalen
dc.contributor.authorKojima, Kenji Ken
dc.contributor.authorVillar, Emilieen
dc.contributor.authorRomac, Sarahen
dc.contributor.authorVeluchamy, Alagurajen
dc.contributor.authorBoccara, Martineen
dc.contributor.authorJaillon, Olivieren
dc.contributor.authorLudicone, Danieleen
dc.contributor.authorBowler, Chrisen
dc.contributor.authorWincker, Patricken
dc.contributor.authorClaverie, Jean-Michelen
dc.contributor.authorOgata, Hiroyukien
dc.date.accessioned2015-12-27T13:27:13Zen
dc.date.available2015-12-27T13:27:13Zen
dc.date.issued2015-11-27en
dc.identifier.citationReverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages 2015 The ISME Journalen
dc.identifier.issn1751-7362en
dc.identifier.issn1751-7370en
dc.identifier.doi10.1038/ismej.2015.192en
dc.identifier.urihttp://hdl.handle.net/10754/592606en
dc.description.abstractGenes encoding reverse transcriptases (RTs) are found in most eukaryotes, often as a component of retrotransposons, as well as in retroviruses and in prokaryotic retroelements. We investigated the abundance, classification and transcriptional status of RTs based on Tara Oceans marine metagenomes and metatranscriptomes encompassing a wide organism size range. Our analyses revealed that RTs predominate large-size fraction metagenomes (>5 μm), where they reached a maximum of 13.5% of the total gene abundance. Metagenomic RTs were widely distributed across the phylogeny of known RTs, but many belonged to previously uncharacterized clades. Metatranscriptomic RTs showed distinct abundance patterns across samples compared with metagenomic RTs. The relative abundances of viral and bacterial RTs among identified RT sequences were higher in metatranscriptomes than in metagenomes and these sequences were detected in all metatranscriptome size fractions. Overall, these observations suggest an active proliferation of various RT-assisted elements, which could be involved in genome evolution or adaptive processes of plankton assemblage.en
dc.language.isoenen
dc.publisherNature Publishing Groupen
dc.relation.urlhttp://www.nature.com/doifinder/10.1038/ismej.2015.192en
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/.en
dc.titleReverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblagesen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentCenter for Desert Agricultureen
dc.identifier.journalThe ISME Journalen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionInformation Génomique et Structurale, UMR7256, CNRS, Aix-Marseille Université, Institut de Microbiologie de la Méditerranée (FR3479), Parc Scientifique de Luminy, Marseille, Franceen
dc.contributor.institutionGenetic Information Research Institute, Los Altos, CA, USAen
dc.contributor.institutionCNRS, UMR 7144, team EPEP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, Franceen
dc.contributor.institutionSorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Place Georges Teissier, FR-Roscoff, Franceen
dc.contributor.institutionEcole Normale Supérieure, PSL Research University, Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Paris, Franceen
dc.contributor.institutionCEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, Evry Cedex, Franceen
dc.contributor.institutionUniversité d’Evry, Evry Cedex, Franceen
dc.contributor.institutionCentre National de la Recherche Scientifique (CNRS), Evry Cedex, Franceen
dc.contributor.institutionLaboratory of Ecology and Evolution of Plankton, Stazione Zoologica Anton Dohrn, Naples, Italyen
dc.contributor.institutionBioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, Japanen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorVeluchamy, Alagurajen
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