Accumulation and rapid decay of non-LTR retrotransposons in the genome of the three-spine stickleback

Eryn Blass, Michael Bell, Stephane Boissinot

Research output: Contribution to journalArticle

Abstract

The diversity and abundance of non-long terminal repeat (LTR) retrotransposons (nLTR-RT) differ drastically among vertebrate genomes. At one extreme, the genome of placental mammals is littered with hundreds of thousands of copies resulting from the activity of a single clade of nLTR-RT, the L1 clade. In contrast, fish genomes contain a much more diverse repertoire of nLTR-RT, represented by numerous active clades and families. Yet, the number of nLTR-RT copies in teleostean fish is two orders of magnitude smaller than in mammals. The vast majority of insertions appear to be very recent, suggesting that nLTRRT do not accumulate in fish genomes. This pattern had previously been explained by a high rate of turnover, in which the insertion of new elements is offset by the selective loss of deleterious inserts. The turnover model was proposed because of the similarity between fish and Drosophila genomes with regard to their nLTR-RT profile. However, it is unclear if this model applies to fish. In fact, a previous study performed on the puffer fish suggested that transposable element insertions behave as neutral alleles. Here we examined the dynamics of amplification of nLTR-RT in the three-spine stickleback (Gasterosteus aculeatus). In this species, the vast majority of nLTR-RT insertions are relatively young, as suggested by their low level of divergence. Contrary to expectations, a majority of these insertions are fixed in lake and oceanic populations; thus, nLTR-RT do indeed accumulate in the genome of their fish host. This is not to say that nLTR-RTs are fully neutral, as the lack of fixed long elements in this genome suggests a deleterious effect related to their length. This analysis does not support the turnover model and strongly suggests that a much higher rate of DNA loss in fish than in mammals is responsible for the relatively small number of nLTR-RT copies and for the scarcity of ancient elements in fish genomes. We further demonstrate that nLTR-RT decay in fish occurs mostly through large deletions and not by the accumulation of small deletions.

Original languageEnglish (US)
Pages (from-to)687-702
Number of pages16
JournalGenome Biology and Evolution
Volume4
Issue number5
DOIs
StatePublished - Sep 26 2012

Fingerprint

Smegmamorpha
Retroelements
terminal repeat sequences
Terminal Repeat Sequences
Gasterosteidae
retrotransposons
spine (bones)
Fishes
Spine
genome
deterioration
Genome
fish
Mammals
turnover
mammal
Tetraodontiformes
mammals
DNA Transposable Elements
Tetraodontidae

Keywords

  • Gasterosteus aculeatus
  • Genome size evolution
  • Non-LTR retrotransposon
  • Retroposon
  • Three-spine stickleback

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

Accumulation and rapid decay of non-LTR retrotransposons in the genome of the three-spine stickleback. / Blass, Eryn; Bell, Michael; Boissinot, Stephane.

In: Genome Biology and Evolution, Vol. 4, No. 5, 26.09.2012, p. 687-702.

Research output: Contribution to journalArticle

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