Published November 27, 2015 | Version v1
Journal article Open

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

Authors/Creators

  • 1. Information Génomique et Structurale, UMR7256, CNRS, Aix-Marseille Université, Institut de Microbiologie de la Méditerranée (FR3479), Parc Scientifique de Luminy, Marseille, France
  • 2. Genetic Information Research Institute, Los Altos, CA, USA
  • 3. CNRS, UMR 7144, team EPEP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
  • 4. Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Paris, France
  • 5. CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, Evry Cedex, France
  • 6. Laboratory of Ecology and Evolution of Plankton, Stazione Zoologica Anton Dohrn, Naples, Italy
  • 7. Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, Japan

Description

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 (45 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.

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Additional details

Funding

European Commission
MICRO B3 - Marine Microbial Biodiversity, Bioinformatics and Biotechnology 287589