title: Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages.
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.
authors.affiliation: Information Génomique et Structurale, UMR7256, CNRS, Aix-Marseille Université, Institut de Microbiologie de la Méditerranée (FR3479), Parc Scientifique de Luminy, Marseille, France.
authors.forename: Magali
authors.initials: M
authors.lastname: Lescot
authors.affiliation: Information Génomique et Structurale, UMR7256, CNRS, Aix-Marseille Université, Institut de Microbiologie de la Méditerranée (FR3479), Parc Scientifique de Luminy, Marseille, France.
authors.forename: Pascal
authors.initials: P
authors.lastname: Hingamp
authors.affiliation: Genetic Information Research Institute, Los Altos, CA, USA.
authors.forename: Kenji K
authors.initials: KK
authors.lastname: Kojima
authors.affiliation: Information Génomique et Structurale, UMR7256, CNRS, Aix-Marseille Université, Institut de Microbiologie de la Méditerranée (FR3479), Parc Scientifique de Luminy, Marseille, France.
authors.forename: Emilie
authors.initials: E
authors.lastname: Villar
authors.affiliation: CNRS, UMR 7144, team EPEP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France.|Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Place Georges Teissier, FR-Roscoff, France.
authors.forename: Sarah
authors.initials: S
authors.lastname: Romac
authors.affiliation: Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Paris, France.
authors.forename: Alaguraj
authors.initials: A
authors.lastname: Veluchamy
authors.affiliation: Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Paris, France.
authors.forename: Martine
authors.initials: M
authors.lastname: Boccara
authors.affiliation: CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, Evry Cedex, France.|Université d'Evry, Evry Cedex, France.|Centre National de la Recherche Scientifique (CNRS), Evry Cedex, France.
authors.forename: Olivier
authors.identifier: http://orcid.org/0000-0002-7237-9596
authors.initials: O
authors.lastname: Jaillon
authors.affiliation: Laboratory of Ecology and Evolution of Plankton, Stazione Zoologica Anton Dohrn, Naples, Italy.
authors.forename: Daniele
authors.identifier: http://orcid.org/0000-0002-7473-394X
authors.initials: D
authors.lastname: Iudicone
authors.affiliation: Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Paris, France.
authors.forename: Chris
authors.initials: C
authors.lastname: Bowler
authors.affiliation: CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, Evry Cedex, France.|Université d'Evry, Evry Cedex, France.|Centre National de la Recherche Scientifique (CNRS), Evry Cedex, France.
authors.forename: Patrick
authors.initials: P
authors.lastname: Wincker
authors.affiliation: Information Génomique et Structurale, UMR7256, CNRS, Aix-Marseille Université, Institut de Microbiologie de la Méditerranée (FR3479), Parc Scientifique de Luminy, Marseille, France.
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Claverie
authors.affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, Japan.
authors.forename: Hiroyuki
authors.identifier: http://orcid.org/0000-0001-6594-377X
authors.initials: H
authors.lastname: Ogata
mesh_terms: D056890:Eukaryota / Q000201:enzymology / Q000235:genetics / Q000302:isolation & purification; D054892:Metagenome; D010802:Phylogeny; D010933:Plankton / Q000201:enzymology* / Q000235:genetics* / Q000378:metabolism; D011387:Prokaryotic Cells / Q000201:enzymology / Q000378:metabolism; D012194:RNA-Directed DNA Polymerase / Q000235:genetics* / Q000378:metabolism; D018626:Retroelements; D012623:Seawater / Q000382:microbiology* / Q000821:virology; D014158:Transcription, Genetic
chemical_list: D018626:Retroelements; D012194:RNA-Directed DNA Polymerase