Genomic Characterization of hox Genes in Senegalese Sole (Solea senegalensis, Kaup 1858): Clues to Evolutionary Path in Pleuronectiformes

Abstract

The Senegalese sole (Solea senegalensis, Kaup 1858), a marine flatfish, belongs to the Pleuronectiformes order. It is a commercially important species for fisheries and aquaculture. However, in aquaculture, several production bottlenecks have still to be resolved, including skeletal deformities and high mortality during the larval and juvenile phase. The study aims to characterize the hox gene clusters in S. senegalensis to understand better the developmental and metamorphosis process in this species. Using a BAC library, the clones that contain hox genes were isolated, sequenced by NGS and used as BAC-FISH probes. Subsequently the hox clusters were studied by sequence analysis, comparative genomics, and cytogenetic and phylogenetic analysis. Cytogenetic analysis demonstrated the localization of four BAC clones on chromosome pairs 4, 12, 13, and 16 of the Senegalese sole cytogenomic map. Comparative and phylogenetic analysis showed a highly conserved organization in each cluster and different phylogenetic clustering in each hox cluster. Analysis of structural and repetitive sequences revealed accumulations of polymorphisms mediated by repetitive elements in the hoxba cluster, mainly retroelements. Therefore, a possible loss of the hoxb7a gene can be established in the Pleuronectiformes lineage. This work allows the organization and regulation of hox clusters to be understood, and is a good base for further studies of expression patterns.

The genomic study of repetitive elements in Solea senegalensis reveals multiple impacts of transposable elements in the evolution and architecture of Pleuronectiformes chromosomes

“…This commercial interest has promoted the increase in genomic resources in the last decade (Robledo et al, 2017;Garcıá-Angulo et al, 2018;Cross et al, 2020;Merlo et al, 2021;Rodrıǵuez et al, 2021;de la Herrań et al, 2023), including an initial version of its genome (Guerrero-Coźar et al, 2021) and a recent improved version (de la Herrań et al, 2023). Due to the absence, until 2023, of a quality sequenced genome in this species, repetitive sequence studies on Senegalese sole had been limited to the sequence analysis of some BAC clones mapped on the chromosomes of the species (Garcıá et al, 2019;Rodrıǵuez et al, 2019;Cross et al, 2020;Rodrıǵuez et al, 2021;Ramıŕez et al, 2022) and the study of TEs in the Hox gene clusters of three flatfish species, including S. senegalensis (Mendizabal-Castillero et al, 2022).…”