Exploring Macquarie perch and golden perch genome annotations
Forty-four Macquarie perch genes found by BRAKER2 were annotated by InterProScan5 to genes/gene families that act as sex-determining genes in other fish species, including amh (anti-Müllerian hormone; g1995 on SEMN01000046), amhr2 ( anti-Müllerian hormone receptor 2 (g4926 on SEMN01000461 and g28883 on SEMN01000098), bcar1 (breast cancer anti-resistance gene; g8496 on SEMN01000123), brca2(breast cancer type 2 susceptibility protein; g21038 on SEMN01000023 and g32091 on SEMN01000434), dmrt1 (doublesex- andmab-3 -related transcription factor 1; g4593 on SEMN01000160), andSOX (Sry -related HMG-box family; 37 genes on 34 scaffolds; Appendix E, Table E1).
Macquarie perch scaffold 633 was found to contain eight genes (Table E3), one of which (g10286; bases 131251- 132300) was annotated to the gene transcription factor SOX (IPR022097), which has the function of regulating DNA-templated transcription (GO:0006355). This gene was located ~38 Kb downstream of the scaffold 633 region containing 11 strongly sex-linked loci (including the 146-bp sexing region 93182-93327; Table 3). About 41 Kb upstream of the 146-bp sexing region was a gene (g10285; bases 35783- 52002) with several domains annotated with protein binding function (GO:0005515) and guanyl-nucleotide exchange factor activity (GO:0005085). The scaffold 633 sex-linked SNP found by DArT (base 43200; Table 2) was located within intron 5 of this gene. The scaffold 633 region 52003-131250, containing the 146-bp sexing region, was not annotated to a gene. Of the other genome-wide Macquarie perch sex-linked SNPs (Tables 2 and 3), one was in a coding region (of the protein DUF3504 of unknown function; gene g30509 on SEMN01000396), and seven were in introns of annotated genes other than known sex-determining ones (Table E4); the other SNPs were not in annotated regions.
Forty-five putative sex-determining genes were observed in golden perch annotations: amh: g25528 on VMKM01002284, amhr: g34189 on VMKM0100047038 and g6203 on VMKM01004095, bcar1: g9675 on VMKM01002618, brca2: g12532 on VMKM01000091 and g16441 on VMKM01000026, dmrt1: g13446 on VMKM01000340, and SOX genes on 36 scaffolds; Table E2). Three of 44 golden perch sex-linked DArT-SNPs mapped to the genome were in the scaffolds containingSOX genes, at a distance of 67-635 Kb from these genes (Table E5).