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Transposable element libraries from 101 fish

Reinar, William B.1; Tørresen, Ole K.1; Nederbragt, Alexander J.1; Matschiner, Michael1; Jentoft, Sissel1; Jakobsen, Kjetill S.1

Research facility: Centre for Ecological and Evolutionary Synthesis*
Published Sep 28, 2023 on Dryad. https://doi.org/10.5061/dryad.4xgxd25g9

Data files

Sep 28, 2023 version files 84.80 MB

Abstract

Repetitive DNA make up a considerable fraction of most eukaryotic genomes. In fish, transposable element (TE) activity has coincided with rapid species diversification. Here, we annotated the repetitive content in 100 genome assemblies, covering the major branches of the diverse lineage of teleost fish. We investigated if TE content correlates with family level net diversification rates and found support for a weak negative correlation. Further, we found that TE proportion correlate to genome size, but not to the proportion of short tandem repeats (STRs), which implies independent evolutionary paths. Marine and freshwater fish have large differences in STR content. The most extreme propagation was found in the genomes of codfish species and Atlantic herring. Such a high density of STRs is likely to increase the mutational load, which we propose could be counterbalanced by high fecundity as seen in codfishes and herring.