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Evolutionary impact of transposable elements on genomic diversity and lineage-specific innovation in vertebrates

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Abstract

Since their discovery, a growing body of evidence has emerged demonstrating that transposable elements are important drivers of species diversity. These mobile elements exhibit a great variety in structure, size and mechanisms of transposition, making them important putative actors in organism evolution. The vertebrates represent a highly diverse and successful lineage that has adapted to a wide range of different environments. These animals also possess a rich repertoire of transposable elements, with highly diverse content between lineages and even between species. Here, we review how transposable elements are driving genomic diversity and lineage-specific innovation within vertebrates. We discuss the large differences in TE content between different vertebrate groups and then go on to look at how they affect organisms at a variety of levels: from the structure of chromosomes to their involvement in the regulation of gene expression, as well as in the formation and evolution of non-coding RNAs and protein-coding genes. In the process of doing this, we highlight how transposable elements have been involved in the evolution of some of the key innovations observed within the vertebrate lineage, driving the group’s diversity and success.

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Abbreviations

ChIP-Seq:

Chromatin immunoprecipitation sequencing

ERV:

Endogenous retrovirus

ESC:

Embryonic stem cell

HTT:

Horizontal transfer of TEs

LINE (or SINE):

Long (or short) interspersed nuclear element

lncRNA:

Long non-coding RNA

LTR:

Long terminal repeat

MYA:

Million years ago

Myr:

Million years

nt:

Nucleotides

TE:

Transposable element

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  1. Domitille Chalopin

    Present address: Department of Genetics, University of Georgia, Athens, Georgia, 30602, USA

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  1. Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France

    Ian A. Warren, Magali Naville, Domitille Chalopin, Perrine Levin, Chloé Suzanne Berger, Delphine Galiana & Jean-Nicolas Volff

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Ian Warren, Magali Naville and Domitille Chalopin contributed equally to this work.

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Warren, I.A., Naville, M., Chalopin, D. et al. Evolutionary impact of transposable elements on genomic diversity and lineage-specific innovation in vertebrates. Chromosome Res 23, 505–531 (2015). https://doi.org/10.1007/s10577-015-9493-5

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