Analysis of Transposable Elements Expressed in the Gonads of the Siberian Sturgeon

  • Frédéric Brunet
  • Alexia Roche
  • Domitille Chalopin
  • Magali Naville
  • Christophe Klopp
  • Denise Vizziano-Cantonnet
  • Jean-Nicolas Volff
Chapter

Abstract

Transposable elements (TEs) are mobile and repeated sequences that are major factors of diversity and evolution in genomes. We report here through the analysis of gonad transcriptomes of the Siberian sturgeon Acipenser baerii, a non-teleost ray-finned fish, that sturgeon genomes contain many families of TEs, which are expressed in gonads and might be involved in the evolution of this divergent fish lineage. The high diversity of TEs observed in sturgeons, which is also found in teleost fish, coelacanth, and amphibians but not in birds and mammals, strongly supports that many TE families were present in ancestral vertebrate genomes. Two types of transposable elements potentially differing in their evolutionary dynamics have been further characterized: DIRS-like retrotransposons, with a single lineage mainly transmitted vertically, and Tc1/mariner DNA transposons, with multiple lineages and the possible involvement of horizontal transfer. This first global analysis is a new step toward the understanding of TE evolution and evolutionary impact in non-teleost ray-finned fish and will help to annotate the upcoming sequences of the large sturgeon genomes.

Keywords

Transposable elements Retrotransposons DNA transposons Whole genome duplications Actinopterygii Teleostei Sturgeons 

Notes

Glossary

TEs

Transposable elements

mobilome

The TE repertoire in a genome

cDNA

Complementary DNA

bp

Base pair

aa

Amino acids

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Frédéric Brunet
    • 1
  • Alexia Roche
    • 1
  • Domitille Chalopin
    • 1
  • Magali Naville
    • 1
  • Christophe Klopp
    • 2
    • 3
  • Denise Vizziano-Cantonnet
    • 4
  • Jean-Nicolas Volff
    • 1
  1. 1.Institut de Genomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1LyonFrance
  2. 2.Genotoul BioInformatic, INRA, UR 875 Unité de Mathématique et Informatique Appliquées, Bioinformatics plateforme Toulouse Midi-Pyrenees, Auzeville, CS 52627Castanet-TolosanFrance
  3. 3.Plate-forme SIGENAE, INRA, GenPhyse, Auzeville, CS 52627Castanet-TolosanFrance
  4. 4.Facultad de Ciencias, Laboratorio de Fisiología de la Reproducción y Ecología de PecesMontevideoUruguay

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