The genomic structure of the highly-conserved dmrt1 gene in Solea senegalensis (Kaup, 1868) shows an unexpected intragenic duplication

Abstract

Knowing the factors responsible for sex determination in a species has significant theoretical and practical implications; the dmrt1 gene ( Doublesex and Mab-3 (DM)-related Transcription factor 1) plays this role in diverse animal species. Solea senegalensis is a commercially important flat fish in which females grow 30% faster than males. It has 2n = 42 chromosomes and an XX / XY chromosome system for sex determination, without heteromorph chromosomes but with sex proto-chromosome. In the present study, we are providing the genomic structure and nucleotide sequence of dmrt1 gene obtained from cDNA from male and female adult gonads. A cDNA of 2027 containing an open-reading frame (ORF) of 1206 bp and encoding a 402 aa protein it is described for dmrt1 gene of S . senegalensis . Multiple mRNA isoforms indicating a high variable system of alternative splicing in the expression of dmrt1 of the sole in gonads were studied. None isoforms could be related to sex of individuals. The genomic structure of the dmrt1 of S . senegalensis showed a gene of 31400 bp composed of 7 exons and 6 introns. It contains an unexpected duplication of more than 10399 bp, involving part of the exon I, exons II and III and a SINE element found in the sequence that it is proposed as responsible for the duplication. A mature miRNA of 21 bp in length was localized at 336 bp from exon V. Protein-protein interacting networks of the dmrt1 gene showed matches with dmrt1 protein from Cynoglossus semilaevis and a protein interaction network with 11 nodes ( dmrt1 plus 10 other proteins). The phylogenetic relationship of the dmrt1 gene in S . senegalensis is consistent with the evolutionary position of its species. The molecular characterization of this gene will enhance its functional analysis and the understanding of sex differentiation in Solea senegalensis and other flatfish.

Integration of Maps Enables a Cytogenomics Analysis of the Complete Karyotype in Solea senegalensis

“…These BAC clones are those on the p arm of metacentric 1 (only with S. maximus), both arms of metacentric 2, and telocentric 10 (only with S. maximus), 11, 12 and 16. Translocations and micro-rearrangements have also been considered to be caused by TEs [35,[54][55][56].…”

A Comprehensive Integrated Genetic Map of the Complete Karyotype of Solea senegalensis (Kaup 1858)

“…These genes are genes frequently associated with sex determination [ 51 , 52 ]. Recently, Cross et al [ 7 ] described an internal duplication of two exons of the dmrt1 gene of S. senegalensis . Such duplication events have often been associated with neofunctionalization of the gene product, which, in this case, the new function could be involved with sex determination.…”

“…This has led several studies to deepen the knowledge of the biology of the Senegalese sole in order to translate it into an improvement for production. Thus, studies related to the life cycle, reproduction, physiology, pathology, genetics and genomics have been carried out [3][4][5][6][7]. However, the genomic data of this species are still scarce compared to other similar species and insufficient to be used in breeding programs.…”

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

“…The Senegalese sole (Solea senegalensis) is among the most important flatfish, with a wide distribution along the eastern coast of the Atlantic Ocean and in the Mediterranean Sea and a high economic value (Imsland et al, 2004;Dıáz-Ferguson et al, 2007, Dıáz-Ferguson et al, 2012. 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).…”