Transposable Elements and Teleost Migratory Behaviour

Abstract

Transposable elements (TEs) represent a considerable fraction of eukaryotic genomes, thereby contributing to genome size, chromosomal rearrangements, and to the generation of new coding genes or regulatory elements. An increasing number of works have reported a link between the genomic abundance of TEs and the adaptation to specific environmental conditions. Diadromy represents a fascinating feature of fish, protagonists of migratory routes between marine and freshwater for reproduction. In this work, we investigated the genomes of 24 fish species, including 15 teleosts with a migratory behaviour. The expected higher relative abundance of DNA transposons in ray-finned fish compared with the other fish groups was not confirmed by the analysis of the dataset considered. The relative contribution of different TE types in migratory ray-finned species did not show clear differences between oceanodromous and potamodromous fish. On the contrary, a remarkable relationship between migratory behaviour and the quantitative difference reported for short interspersed nuclear (retro)elements (SINEs) emerged from the comparison between anadromous and catadromous species, independently from their phylogenetic position. This aspect is likely due to the substantial environmental changes faced by diadromous species during their migratory routes.

Keywords: environmental adaptation; fish; genome evolution; transposable elements.

Figure 1

Cladogram showing the relationships between analysed species. Main clades are reported above the branches. 1R, 2R, and 3R whole genome duplication (WGD) events are reported, and the light-blue star indicates species that have undergone 4R-specific events. Species belonging to Actinopterygii are shown in light blue. The cladogram was modified from Betancur-R et al. [44]. The percentages of total transposable elements (TEs) masked in the genomes of the studied species are shown on the right-hand side. Each bar displays the percentage of the main TE types: DNA transposons in yellow; LTR retroelements in grey; SINE retroelements in orange; LINE retroelements in dark blue; and unclassified elements in light blue.

Figure 2

Relative abundance of TE types in the mobilome of the fish species analysed. The histogram shows the relative abundance of each TE type in the mobilome of two non-ray finned fish and 22 actinopterygians. The migratory behaviour of Actinopterygii is indicated.

Figure 3

Venn diagrams obtained by variation partitioning analyses (VPA) using redundancy analysis (RDA). The partition of the variation of a response variable (X) between two sets of explanatory variables (X1 and X2) is shown. Each circle represents the portion of variation accounting for an explanatory variable or a combination of the explanatory matrices. The intersection between the two circles represents the amount of variation explained by both variables X1 and X2 [45]. (A): the response variable (X) is the quantitative difference reported for SINE retroelements from the comparison between anadromous and catadromous fish species; the explanatory variable X1 represents the migration and the explanatory variable X2 indicates the sequence divergence obtained by p-distance matrix using 16S rDNA. (B): the response variable (X) is the quantitative difference reported for DNA transposons from the comparison between catadromous and amphidromous fish species; the explanatory variable X1 represents the migration and the explanatory variable X2 indicates the sequence divergence obtained by p-distance matrix using 16S rDNA.

Figure 4

Cladogram with repeat landscape plots. The cladogram reported on the left summarises the phylogenetic relationships among the species analysed in this study. The graphs displayed on the right report the repeat landscape plots obtained by Kimura distance-based copy divergence analyses of transposable elements for each species. The repeat landscape plots are reported at higher resolution in Supplementary File S1.