Chromosome anchoring in Senegalese sole (Solea senegalensis) reveals sex-associated markers and genome rearrangements in flatfish

Abstract

The integration of physical and high-density genetic maps is a very useful approach to achieve chromosome-level genome assemblies. Here, the genome of a male Senegalese sole (Solea senegalensis) was de novo assembled and the contigs were anchored to a high-quality genetic map for chromosome-level scaffolding. Hybrid assembled genome was 609.3 Mb long and contained 3403 contigs with a N50 of 513 kb. The linkage map was constructed using 16,287 informative SNPs derived from ddRAD sequencing in 327 sole individuals from five families. Markers were assigned to 21 linkage groups with an average number of 21.9 markers per megabase. The anchoring of the physical to the genetic map positioned 1563 contigs into 21 pseudo-chromosomes covering 548.6 Mb. Comparison of genetic and physical distances indicated that the average genome-wide recombination rate was 0.23 cM/Mb and the female-to-male ratio 1.49 (female map length: 2,698.4 cM, male: 2,036.6 cM). Genomic recombination landscapes were different between sexes with crossovers mainly concentrated toward the telomeres in males while they were more uniformly distributed in females. A GWAS analysis using seven families identified 30 significant sex-associated SNP markers located in linkage group 18. The follicle-stimulating hormone receptor appeared as the most promising locus associated with sex within a region with very low recombination rates. An incomplete penetrance of sex markers with males as the heterogametic sex was determined. An interspecific comparison with other Pleuronectiformes genomes identified a high sequence similarity between homologous chromosomes, and several chromosomal rearrangements including a lineage-specific Robertsonian fusion in S. senegalensis.

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

“…Interestingly, non-synonymous variants were mostly concentrated at exon 14 and to an extent at exon 1, which are part of its intracellular and extracellular domains, respectively, related to signal transduction and hormone reception. Moreover, we could not detect evidence of a duplication of the fshr gene in the Senegalese sole male genome reported by Guerrero-Cozar et al (2021), and therefore, the fshry allele appears to be the key factor for the male fate of the undifferentiated primordium. A similar SD mechanism has been reported in gray mullet, where an fshry allele including only two non-synonymous variants was identified as responsible for the male fate of the undifferentiated primordium (Curzon et al, 2021).…”

“…Guerrero-Cozar et al (2021) reported a broad genomic region (1.4 Mb) associated with sex at SseLG18 of S. senegalensis (Sse C12 in our study) using five full-sib families, compatible with a nascent XX / XY system. They suggested a SD mechanism with incomplete penetrance influenced by environmental factors since sex association was incomplete, and proposed fshr as the most promising master SD gene considering its role in gonad development and previous data from other species (Curzon et al, 2021).…”

“…These 21 scaffolds were associated to the corresponding chromosomes of this species using a BAC-FISH approach (average 6.6 BACs / chromosome), thus providing a sound reference for comparative genomics and for studying the genetic architecture of relevant traits, such as sex determination. The new assembly displayed a major one to one chromosome correspondence with the recently reported genome by Guerrero-Cozar et al (2021), and most of the discordances were related to orientation of minor scaffolds due to the higher fragmentation and less contiguity of the previous assembly (∼1937 scaffolds; 90 % of the assembly integrated in chromosomes). This upgraded Senegalese sole genome allowed the identification and annotation of 24,264 protein-coding genes encoding for 37,259 unique protein products (85% with functional annotation), along with 52,888 non-coding RNAs (6,871 long non-coding and 46,017 small RNAs).…”

“…The syntenic relationships among the chromosomes of the six flatfish species were represented using ggsankey (https://github.com/davidsjoberg/ggsankey), while syntenic comparisons by pairs were drawn using the R package circlize (Gu et al, 2014). Finally, we compared the Senegalese sole genome here reported with the previous one by Guerrero-Cozar et al (2021) using LASTZ (Harris, 2007) (options “--notransition -- step=400 --nogapped --format=rdotplot”).…”

“…This rapid diversification has also led to a large variety of SD mechanisms, with diverse master SD genes and non-orthologous SD regions in all species analysed to date (Luckenbach et al, 2011; Martínez et al, 2021). The genomes of flatfish are compact (∼500-700 Mb; Robledo et al, 2017; Lü et al, 2021), which has facilitated the achievement of chromosome-level genome assemblies in species from several families of the order (Guerrero-Cózar et al, 2021; Lü et al, 2021).…”