Identification of the master sex determining gene in Northern pike (Esox lucius) reveals restricted sex chromosome differentiation

Abstract

Teleost fishes, thanks to their rapid evolution of sex determination mechanisms, provide remarkable opportunities to study the formation of sex chromosomes and the mechanisms driving the birth of new master sex determining (MSD) genes. However, the evolutionary interplay between the sex chromosomes and the MSD genes they harbor is rather unexplored. We characterized a male-specific duplicate of the anti-Müllerian hormone ( amh) as the MSD gene in Northern Pike ( Esox lucius ), using genomic and expression evidence as well as by loss-of-function and gain-of-function experiments. Using RAD-Sequencing from a family panel, we identified Linkage Group (LG) 24 as the sex chromosome and positioned the sex locus in its sub-telomeric region. Furthermore, we demonstrated that this MSD originated from an ancient duplication of the autosomal amh gene, which was subsequently translocated to LG24. Using sex-specific pooled genome sequencing and a new male genome sequence assembled using Nanopore long reads, we also characterized the differentiation of the X and Y chromosomes, revealing a small male-specific insertion containing the MSD gene and a limited region with reduced recombination. Our study reveals an unexpectedly low level of differentiation between a pair of sex chromosomes harboring an old MSD gene in a wild teleost fish population, and highlights both the pivotal role of genes from the amh pathway in sex determination, as well as the importance of gene duplication as a mechanism driving the turnover of sex chromosomes in this clade.

Loss of genetic variation and sex determination system in North American northern pike characterized by whole-genome resequencing

“…In alignment with Pan et al, 2020, , we were able to detect a sex-specific signal within our population from Chatanika River, Alaska, which was comprised of 5 females and 5 males, sexed by visual observation of ovaries (female) or testes (male). In agreement with (Pan et al, 2019), we detected male-specific heterozygosity on linkage group 24 through both DAPC and kmer analysis (Figure 5A, 5E). This signal consisted of 3,552 male specific SNPs spanning a 500 kb region between 650 -1150 kb on linkage group 24.…”

“…Chromosome-length scaffolds were assigned to linkage groups using the same linkage map utilized in prior assemblies (Rondeau et al, 2014). As linkage groups were oriented by density of inter-chromosomal contacts, repeat masking (using methods and repeat library in (Rondeau et al, 2014) -results summarized in Supplementary Table 1) reveals the greatest density of repeat elements at the 3' end of the chromosome (Supplementary Annotation of genomes described in this work was performed by the NCBI eukaryotic genome annotation pipeline using previously utilized (Rondeau et al, 2014) and recently released (Pan et al, 2019) RNA-seq and EST data (Leong et al, 2010). In version 4, this encompasses 24,843 protein-coding genes across the genome.…”

“…As prices decrease, we are also likely to see the introduction of assemblies with specific uses rather than a single reference genome. Indeed, the work of Pan et al (Pan et al, 2019) produced a longread assembly of a European male northern pike, with the aim of characterizing the region of the sex-determination gene within the genome. As such works are assembled and released, it is likely that the genome (or perhaps genomes, given the two biological sources) presented here will be North American representatives incorporated into a pan-genome for the species, with additional assemblies from European and Asian lineages being added to represent the full diversity of the Holarctic species.…”

“…A male-specific duplicated gene copy of the anti-Mullerian hormone, amhby, has been identified as the MSD gene responsible for male differentiation in northern pike from Europe (Pan et al, 2019). However, previous studies of North American pike (Rondeau et al, 2014) had found no markers associated with sex and early discussions with the authors of Pan et al, (2020) suggested that amhby was absent in North America.…”

Characterization of a Y‐specific duplication/insertion of the anti‐Mullerian hormone type II receptor gene based on a chromosome‐scale genome assembly of yellow perch, Perca flavescens

“…To validate the male specificity of this potential Y-specific insertion, we designed primers specific for both amhr2by and This complete sex-linkage result makes the yellow perch amhr2by a strong candidate as a sex-determining gene. Interestingly, anti-Mullerian hormone (Amh) has been also characterized as a male-promoting gene in zebrafish (Yan et al, 2019) and as a master sex-determining gene both in Patagonian pejerrey (Hattori et al, 2012), Nile tilapia (Li et al, 2015) and northern pike (Pan et al, 2019). Amh belongs to the transforming growth factor beta (TGF-β) family that contains structurally related growth factors involved in many differentiation processes.…”