Characterization of a male specific region containing a candidate sex determining gene in Atlantic cod

Abstract

The genetic mechanisms determining sex in teleost fishes are highly variable and the master sex determining gene has only been identified in few species. Here we characterize a male-specific region of 9 kb on linkage group 11 in Atlantic cod (Gadus morhua) harboring a single gene named zkY for zinc knuckle on the Y chromosome. Diagnostic PCR test of phenotypically sexed males and females confirm the sex-specific nature of the Y-sequence. We identified twelve highly similar autosomal gene copies of zkY, of which eight code for proteins containing the zinc knuckle motif. 3D modeling suggests that the amino acid changes observed in six copies might influence the putative RNA-binding specificity. Cod zkY and the autosomal proteins zk1 and zk2 possess an identical zinc knuckle structure, but only the Y-specific gene zkY was expressed at high levels in the developing larvae before the onset of sex differentiation. Collectively these data suggest zkY as a candidate master masculinization gene in Atlantic cod. PCR amplification of Y-sequences in Arctic cod (Arctogadus glacialis) and Greenland cod (Gadus macrocephalus ogac) suggests that the male-specific region emerged in codfishes more than 7.5 million years ago.

Genome-wide RAD sequencing to identify a sex-specific marker in Chinese giant salamander Andrias davidianus

“…In Gadus morhua, male-specific region of 9 kb was mapped on linkage group 11 annotating a single gene named zkY on the Y chromosome. Expression of zkY was high level in the developing larvae before the onset of sex differentiation [39]. In Rana clamitans , 13 sex-linked SNP loci and eight loci associated with males were identified by Diversity Arrays Technology [40, 41], which employs a combination of genome complexity reduction and next-generation sequencing similar to RAD-seq and genotyping-by-sequencing methods [42].…”

Young sex chromosomes in plants and animals

“…Selection favouring closer linkage between two mutations occurs only if the mutations initially recombine; if they are within the same gene, they will be closely linked from the time they originated, again forming a small sex‐linked region. Single‐gene systems have been discovered in several fish, including fugu (Kamiya et al ., ) and Atlantic salmon (Kirubakaran et al ., ), and could be involved in plants with homomorphic sex chromosomes, which appear to be common among angiosperms (Westergaard, ). A single‐gene system can evolve via two mutations, one of which becomes fixed in the species (as appears to have happened in the persimmon, see the earlier section headed 'Other mutation types that could generate dioecy').…”

“…However, the existence of strata is still difficult to test, as exemplified by uncertainties in sex chromosomes of fish such as the Atlantic cod (Kirubakaran et al ., ) and some cichlid species (Gammerdinger & Kocher, ). Strata are most likely to be detectable in moderately young sex chromosomes.…”

Structural genomic variation leads to genetic differentiation in Lake Tanganyika's sardines

“…In Atlantic cod and herring populations, low genome-wide divergence is interspersed with highly divergent inverted regions. These inversions in cod distinguish between resident and migrating ecotypes (Berg et al, 2017;Kirubakaran et al, 2016) and males and females (Kirubakaran et al, 2019), and in herring, they separate spring and fall spawners (Lamichhaney et al, 2017;Martinez Barrio et al, 2016;Pettersson et al, 2019). Additionally, inverted genomic regions in sticklebacks are involved in the divergence between lake and stream ecotypes (Marques et al, 2016;Roesti, Kueng, Moser, & Berner, 2015).…”

“…Pelagic habitats allow for high dispersal rates due to the lack of predominant physical barriers. Well-known examples of species from pelagic habitats that carry chromosomal inversions or sexlinked genomic differentiation include Atlantic cod (Gadus moruha; Berg et al, 2017;Kirubakaran et al, 2019;Kirubakaran et al, 2016) and Atlantic herring (Clupea harengus; Lamichhaney et al, 2017;Martinez Barrio, Lamichhaney, & Fan, 2016;Pettersson et al, 2019).…”