A chromosome‐level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex‐determining gene in the flatfish Solea senegalensis

Abstract

Sex determination (SD) shows huge variation among fish and a high evolutionary rate, as illustrated by the Pleuronectiformes (flatfishes). This order is characterized by its adaptation to demersal life, compact genomes and diversity of SD mechanisms. Here, we assembled the Solea senegalensis genome, a flatfish of great commercial value, into 82 contigs (614 Mb) combining long-and short-read sequencing, which were next scaffolded using a highly dense genetic map (28,838 markers, 21 linkage groups),

Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure

“…In this sense, a recent study by Ferchaud et al [ 103 ] propose the SRY-Box Transcription Factor 2 ( Sox2 ) as a potential candidate not only in Greenland halibut but also in other flatfishes. Other gene candidates include follicle stimulating hormone receptor ( fshr ) in Senegalese sole [ 104 ], bone morpho-genetic protein receptor type1B ( bmpr1ba ) in Hippoglossus stenolepi [ 99 ], Forkhead box L2 ( Foxl2) and Doublesex and mab-3 related transcription factor 1 ( dmrt1) in Japanese flounder ( Paralichthys olivaceus ) [ 105 ], and Gonadal soma-derived factor ( gsdf ) in Atlantic Halibut ( Hippoglossus hippoglossus ) [ 106 , 107 ]. Furthermore, another recent study conducted in the Japanese flounder, utilizing amhy -mutant flounders generated thorough the CRISPR-Cas9 system technology, demonstrated the crucial role of amhy for testicular formation in this species [ 108 ].…”

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

“…In 2021, in the first version of the species' genome (Guerrero-Coźar et al, 2021), during the genome annotation process, a brief reference is made to the global content of repetitive sequences, giving a value of 23.41% for a female linkage map and 23.55% for the male one, without any additional contribution or evaluation in relation to these sequences and their classes, types, superfamilies, or families. Subsequently, in a new, more complete and improved version of the genome (de la Herrań et al, 2023), more up-to-date general data on repetitive elements were obtained. To do this, the authors created a library of repetitive elements directly from non-assambled sequencing reads (Illumina), using an experimental design based on the de novo analysis performed by the RepeatExplorer platform (Novaḱ et al, 2020).…”

“…Despite the scarce amount of genome analyzed, limited by the small portion of each chromosome contained in these BACs and of genome studied, it was possible to observe certain differences in the abundance of elements in BACs belonging to different chromosomes and different intrachromosomal location (Garcıá et al, 2019;Rodrıǵuez et al, 2019, Rodrıǵuez et al, 2021Ramıŕez et al, 2022). However, it was only after the publication of the recent complete whole-genome sequence of S. senegalensis (de la Herrań et al, 2023), we have been able to completely analyze the abundance of repetitive elements in each of the 21 pairs of chromosomes of the species. Although the content of the different types of elements in general seemed to show a similar behavior, with homogenized values in the chromosomes, the study by superfamilies did show differences in coverage between chromosomes, very notable in the case of satellites and Helitrons.…”

“…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).…”

Editorial 2024

“…Useful guidance was provided for data analyses such estimating admixture from genomic data without a reference assembly (Garcia‐Erill et al., 2023), and simulating phenotypic plasticity in context of adaptive capacity and extinction risk (Seaborn et al., 2023). The utility of reference genomes for yielding biological insights were evident in studies such as (de la Herrán et al., 2023), as well as the importance of closely related genome assemblies and pangenomes to account for intraspecific genomic variation (Puente‐Sánchez et al., 2023; Thorburn et al., 2023). Advances in eDNA techniques were illustrated by several studies including a novel approach that reconstructed phylogenies of multiple species from water samples (Tsuji et al., 2023).…”