Genome and Sex Determination Mechanism In Half-Smooth Tongue Sole (Cynoglossus semilaevis)

Whole-genome sequencing and assembly were completed in a flatfish, half-smooth tongue sole (Cynoglossus semilaevis). The genome size was about 520Mb which contain 53Mb repeat sequence. We predicted 20,834 genes, with a mean coding sequence size of 1,535 bp and an average of 9 exons per gene. In total, we found 30,961 orthologous clusters that were shared by at least two species, and 5,799 clusters that were shared by all four species. There were 4,972 tongue sole-specific genes, which are more than other three fish-specific genes. Several sex-chromosome (W and Z) specific genes were identified and cloned, and their temporal and spacial expression were analyzed. A high density SNP genetic map of half-smooth tongue sole were developed using RAD-seq technique. Parents were resequenced by Heq2000 with sequencing depth of 16.8 X and 15.1X for male and female, respectively. 894,373 SNP loci were obtained, of which 407,084 heterozygous loci for male, 397,300 heterozygous loci for female, 89,989 heterozygous loci for both, representing the genome coverage of 96.2%, 96.4% and 95.3%, respectively. The 216 individuals genotype of F1 progeny were attained. Finally, a total of 12,142 SNP markers by scaffolds were obtained after the separation ratio test (P=0.05). The high resolution genetic map contains 22 linkage groups (20 autosomes and 2 sex chromosomes) with the average marker for LG is 552 covering the 422,204 kb length using the JoinMap 4.0. Chromosome genomic maps were constructed by anchoring  scaffolds to 21 chromosomes by means of SSR and SNP markers on genetic linkage map.