Exploring annotations of sex-linked SNPs and seeking candidate sex-determining genes in reference genomes
We used genome organization and functional annotations for Macquarie perch and golden perch to test whether sex-linked SNPs were located in gene regions, and whether Macquarie perch scaffold 633 has annotated genes that might play a role in sex-determination. We also looked for the presence and location in the perch genomes of sex-determining genes known from teleost fish, searching InterProScan5 output for amh , anti-Mullerian hormone, amhr, anti-Mullerian hormone receptor,bcar1 , breast cancer anti-resistance, brca2 , breast cancer type 2 susceptibility protein, dmrt1 , doublesex- andmab-3 -related transcription factor 1, dmY, dm-W, dmW, gsdfY, gonadal soma derived growth factor, sdY and SOX(Bao et al., 2019; Graves, 2013; Rodríguez-Marí et al., 2011) and Gene Ontology term GO:0007530 (biological process: sex determination) and its child terms (https://www.ebi.ac.uk/QuickGO/term/GO:0007530).