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).