Mobile Elements in Ray-Finned Fish Genomes

Abstract

Ray-finned fishes (Actinopterygii) are a very diverse group of vertebrates, encompassing species adapted to live in freshwater and marine environments, from the deep sea to high mountain streams. Genome sequencing offers a genetic resource for investigating the molecular bases of this phenotypic diversity and these adaptations to various habitats. The wide range of genome sizes observed in fishes is due to the role of transposable elements (TEs), which are powerful drivers of species diversity. Analyses performed to date provide evidence that class II DNA transposons are the most abundant component in most fish genomes and that compared to other vertebrate genomes, many TE superfamilies are present in actinopterygians. Moreover, specific TEs have been reported in ray-finned fishes as a possible result of an intricate relationship between TE evolution and the environment. The data summarized here underline the biological interest in Actinopterygii as a model group to investigate the mechanisms responsible for the high biodiversity observed in this taxon.

Keywords: genome evolution; ray-finned fishes; transposable elements.

Figure 1

On the left: cladogram showing the relationships of bony fishes (modified from Betancur-R et al. [7]), with the relative DNA content from the genome size database [6]. The teleost orders lacking genome size information are shown in red. Whole-genome duplications (WGDs) are shown in blue: WGD 1R and 2R occurred in the common ancestor of vertebrates; WGD 3R occurred in the common ancestor of teleosts. The blue stars indicate taxa that underwent further independent WGD events. On the right: a separated cladogram of the Eupercaria clade with its relative nuclear DNA content. Order-level incertae sedis (O level in this figure) includes families awaiting evidence to clarify their phylogenetic status [7].

Figure 2

Mobile genetic element classification based on transposition mechanisms (according to Wicker et al. [153]). The main structural components of the elements are reported on the right (modified from Makalowsky et al. [155]).