Screening a new European hake (Merluccius merluccius) chromosome-level genome assembly suggests an XX/XY sex-determining system driven by the SRY-box transcription factor 3 (sox3)

Abstract

Sex determination is exceptionally diverse and shows a high evolutionary rate in fish. European hake (Merluccius merluccius) is a species of great commercial value distributed throughout European coasts, which displays a significant sexual growth dimorphism. We present a chromosome-level genome of M. merluccius, composed of 215 contigs using long- and short-read sequencing, further scaffolded into the species' 21 chromosomes using Hi-C technique (715 Mb). RNA-seq on several tissues from pooled individuals improved annotation (26,625 protein-coding genes and 11,083 ncRNAs). Five males and 5 females from an Atlantic population were re-sequenced at 30× depth to look for association with sex across the whole genome. Genetic differentiation between males and females (FST) and intrapopulation fixation index (FIS) pointed to a region on chromosome 9 spanning ∼10 Mb which included several genes related to gonad differentiation and showed strong linkage disequilibrium associated with a putative inversion. Near sox3 gene (∼25 kb), SNPs were mostly heterozygous in males and homozygous in females, consistent with an XX/XY sex-determining (SD) system. These SNP markers were validated in a larger sample of 56 males and 63 females from the same population using MassARRAY. Other genomic regions that were differentiated between males and females and suggestive of sexual conflict were also explored across the genome. Results support a candidate master SD gene in M. merluccius and indicate some differentiated regions potentially under sexual conflict. This information will be useful for the fisheries management of M. merluccius in the context of climate change, where noninvasive sex identification tools are essential.

Keywords: MassARRAY; genetic differentiation; genome assembly; intraspecific variation; sex-determination evolution; sexual conflict; whole-genome sequencing.

Fig. 1.

Snail plot showing the main features of the M. merluccius genome assembly.

Fig. 2.

Screening of genetic differentiation (F_ST) and intrapopulation fixation index (F_IS) across chromosome 9 in an Atlantic population of M. merluccius subdivided by sex: a) most associated chromosome 9 region; b) zoom where the main MSD gene is located; c) genotypes of 5 female (upper rows; 100,100) and 5 male (bottom rows; mostly 100,120) in the most associated region; arrows point to extreme F_ST and F_IS values.

Fig. 3.

Linkage disequilibrium r² values (color scale) and their P-values between pairs of loci across the most consistent region associated with sex at chromosome 9 of M. merluccius. The codes of SNPs represent their position in Mb across C9.

Fig. 4.

Alignment of chromosome 9 from the M. merluccius MmG genome with the homologous chromosome 8 from the MmN genome (x-axis values).