A Y-linked anti-Müllerian hormone type-II receptor is the sex-determining gene in ayu, Plecoglossus altivelis

Abstract

Whole-genome duplication and genome compaction are thought to have played important roles in teleost fish evolution. Ayu (or sweetfish), Plecoglossus altivelis, belongs to the superorder Stomiati, order Osmeriformes. Stomiati is phylogenetically classified as sister taxa of Neoteleostei. Thus, ayu holds an important position in the fish tree of life. Although ayu is economically important for the food industry and recreational fishing in Japan, few genomic resources are available for this species. To address this problem, we produced a draft genome sequence of ayu by whole-genome shotgun sequencing and constructed linkage maps using a genotyping-by-sequencing approach. Syntenic analyses of ayu and other teleost fish provided information about chromosomal rearrangements during the divergence of Stomiati, Protacanthopterygii and Neoteleostei. The size of the ayu genome indicates that genome compaction occurred after the divergence of the family Osmeridae. Ayu has an XX/XY sex-determination system for which we identified sex-associated loci by a genome-wide association study by genotyping-by-sequencing and whole-genome resequencing using wild populations. Genome-wide association mapping using wild ayu populations revealed three sex-linked scaffolds (total, 2.03 Mb). Comparison of whole-genome resequencing mapping coverage between males and females identified male-specific regions in sex-linked scaffolds. A duplicate copy of the anti-Müllerian hormone type-II receptor gene (amhr2bY) was found within these male-specific regions, distinct from the autosomal copy of amhr2. Expression of the Y-linked amhr2 gene was male-specific in sox9b-positive somatic cells surrounding germ cells in undifferentiated gonads, whereas autosomal amhr2 transcripts were detected in somatic cells in sexually undifferentiated gonads of both genetic males and females. Loss-of-function mutation for amhr2bY induced male to female sex reversal. Taken together with the known role of Amh and Amhr2 in sex differentiation, these results indicate that the paralog of amhr2 on the ayu Y chromosome determines genetic sex, and the male-specific amh-amhr2 pathway is critical for testicular differentiation in ayu.

An ancient truncated duplication of the anti‐Müllerian hormone receptor type 2 gene is a potential conserved master sex determinant in the Pangasiidae catfish family

“…In our study, based on chromosome-scale genome assemblies of many Pangasiid species, transcriptomic data (Pasquier et al, 2016) and sex-linkage analyses, we identified a male-specific duplication of the amhr2 (amhr2by) gene as a potentially conserved male MSD gene in that fish family. The role of Amhr2 as an MSD gene has been functionally characterized in the tiger pufferfish, Takifugu rubripes and ayu, Plecoglossus altivelis (Kamiya et al, 2012;Nakamoto et al, 2021), and strongly suggested by sex-linkage information in common seadragon, Phyllopteryx taeniolatus, alligator pipefish, Syngnathoides biaculeatus (Qu et al, 2021), other species of pufferfishes (Duan et al, 2021;Gao et al, 2020;Kamiya et al, 2012) and yellow perch, Perca flavescens (Feron et al, 2020). In addition, the anti-Müllerian hormone, Amh, which is the cognate ligand of AmhR2, has also been demonstrated or suggested as an MSD gene in a few fish species (Hattori et al, 2012;Li et al, 2015;Pan et al, 2019Pan et al, , 2021Song et al, 2021).…”

Molecular parallelism in the evolution of a master sex‐determining role for the anti‐Mullerian hormone receptor 2 gene (amhr2) in Midas cichlids

“…The duplication and origin of amhr2Y pre‐dates the split between Amphilophus and Archocentrus , where it has undergone a turnover and secondary rearrangement. Y‐specific copies of amhr2 have emerged at least five times independently as the MSD gene in teleosts (Kamiya et al, 2012; Nakamoto et al, 2021; Qu et al, 2021; Feron et al, 2020; see Table ). We successfully generated a high‐contiguity haplotypic assembly of a male and assembled the complete YSR using a combination of PacBio HiFi and Bionano optical maps.…”

“…However, the discovery and assembly of SDRs has been facilitated recently due to advances in long‐read sequencing technologies (Palmer et al, 2019; Sember et al, 2021). Long‐read methodologies are especially useful to assemble SDRs, as they generate scaffolds spanning complex genomic regions (Fraser et al, 2020; Nakamoto et al, 2021; Peichel et al, 2020; Qu et al, 2021; Tao, Xu, et al, 2021; Xue et al, 2021).…”

“…The wide spectrum of sex‐determining mechanisms found among closely related species (Nagahama et al, 2021) makes fishes well‐suited models for studying the initial steps during sex chromosome evolution and also to test for molecular parallelism in the origin of master sex‐determining (MSD) genes (Böhne et al, 2019; Godwin & Roberts, 2018). Several MSD genes have already been identified in teleosts, including dmrt1Y ( Oryzias latipes ), sox3 ( Oryzias dancena ), gsdfy ( Oryzias luzonensis ), amhy ( Oreochromis niloticus ) and amhr2Y ( Takifugu rubripes , Perca flavecens , Percoglossus altivelis , Phyllopteryx taeniolatus and Syngnathoides biaculeatus ) (Duan et al, 2021; Feron et al, 2020; Gao et al, 2020; Ieda et al, 2018; Kamiya et al, 2012; Li et al, 2015; Myosho et al, 2012; Nakamoto et al, 2021; Nanda et al, 2002; Qu et al, 2021; Takehana et al, 2014). Although the variety of MSD genes is daunting, the repeated involvement of many of these suggests a large degree of molecular parallelism and that the evolution of novel sex‐determiners is predictable.…”

Sex determination mechanisms and sex control approaches in aquaculture animals

“…Classic theory predicts that homomorphic proto sex chromosomes evolved from ordinary autosomes by acquiring sex-determining gene/genes. Sex-determining gene/genes can be derived from gene mutation (Kamiya et al, 2012;Koyama et al, 2019), gene duplication (Li et al, 2015), and gene translocation (Nakamoto et al, 2021). Subsequently, sexually antagonistic alleles (genes with different fitness in males and females) accumulate around sexdetermining gene/genes and spread along the sex chromosomes.…”