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.
Highlights
The integration of physical and high-density genetic maps is a very useful approach to achieve chromosome-level genome assemblies
Linkage mapping studies were mainly based on microsatellite (SSR) and AFLP m arkers[1,2]; they recently reached a milestone with the development of genotyping methods based on cost-effective massive parallel sequencing
The large arrays of repeated sequences and the degree of conservation for some tandem repeats families widely distributed across the genome still remain a major obstacle for most de novo assembly algorithms, resulting in fragmented scaffolds or even misassembled sequences within chimeric contigs
Summary
The integration of physical and high-density genetic maps is a very useful approach to achieve chromosome-level genome assemblies. 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. An increasing number of high-density genetic maps is nowadays reported in non-model organisms including aquaculture fish[3,4]. These maps have proven to be useful to provide new clues on genome evolution and speciation between closely related lineages, and to unravel the genetic architecture of both simple Mendelian and complex quantitative traits in many fish species, facilitating marker-assisted selection in a quaculture[5,6]. Integrated genetic and physical maps are important genomic resources to understand chromosome evolution in flatfish
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