Study on sex-linked region and sex determination candidate gene using a high-quality genome assembly in yellow drum

Yellow drum is marine fish species distributed in East Asia, exhibiting a sex-dependent dimorphic growth pattern where females grow much faster than males. The sex determination candidate gene and molecular mechanism were still unclear in yellow drum. The interpretation of sex chromosome sequences could shed light on sex determination. Herein, using high-fidelity (HiFi) reads generated with the PacBio circular consensus sequencing mode, we assembled and annotated a male genome of the yellow drum. The genome sequence assembly has a contig N50 size of 22.37 Mb and 98.17% of sequence length of contigs can be assigned to 24 chromosomes via Hi-C interaction data. Fst analysis demonstrated that the genetic divergence regions on sex chromosome occupied 2/3 of sex chromosome. The site with genotypes concordance (the male is heterozygous and female is homozygous) reached 100% in both males and females spanning from 14.9 to 24.9 Mb on sex chromosome, this 10 Mb region was designed as sex determination region (SDR). We integrated the RNAseq data generated with gonads of early development larvae and analyzed the expression of the genes located in SDR, suggested that dmrt1 might play as sex determination key gene in males of yellow drum. Subsequently, we screened out a Y chromosome contig (~1.4 Mb) using a sex-linked marker. We found that there are two tandem dmrt1 genes in yellow drum, designated as dmrt1a and dmrt1b, and dmrt1b harbors a premature stop codon. A male-specific 438-bp deletion in the promoter of dmrt1a was successfully developed as a sex specific marker. Our study laid an important foundation for clarifying the sex determination mechanism in yellow drum and accelerating the production of all-female population. • A high-quality genome has been assembled using HiFi reads and a sex-linked region was mapped in yellow drum. • Dmrt1 was found to be a possible sex-determining gene. • A 438-bp deletion in the promoter of dmrt1 was developed as a new sex-specific marker.