Evolutionary dynamics of DIRS-like and Ngaro-like retrotransposons in Xenopus laevis and Xenopus tropicalis genomes

Abstract

Anuran genomes have a large number and diversity of transposable elements, but are little explored, mainly in relation to their molecular structure and evolutionary dynamics. Here, we investigated the retrotransposons containing tyrosine recombinase (YR) (order DIRS) in the genome of Xenopus tropicalis and Xenopus laevis. These anurans show 2n = 20 and the 2n = 36 karyotypes, respectively. They diverged about 48 million years ago (mya) and X. laevis had an allotetraploid origin (around 17-18 mya). Our investigation is based on the analysis of the molecular structure and the phylogenetic relationships of 95 DIRS families of Xenopus belonging to DIRS-like and Ngaro-like superfamilies. We were able to identify molecular signatures in the 5' and 3' non-coding terminal regions, preserved open reading frames (ORFs) and conserved domains that are specific to distinguish each superfamily. We recognize two ancient amplification waves of DIRS-like elements that occurred in the ancestor of both species and a higher density of the old/degenerate copies detected in the X. laevis. X. tropicalis showed more recent amplification waves estimated around 16 mya and 3.2 mya and corroborate with high diversity-level of families in this species and with transcriptional activity evidence. Ngaro-like elements presented less diversity and quantity in the genomes, although potentially active copies were also found. Our findings highlight a differential diversity-level and evolutionary dynamics of the YR retrotransposons in the diploid X. tropicalis and X. laevis species expanding our comprehension of the behavior of these elements in both genomes during the diversification process