Genome assembly and annotation for Macquarie perch and golden perch
The assembled genome for Macquarie perch (NCBI WGS Project accession SEMN01) had a size of 675.98 Mb comprising 2,962 scaffolds (scaffold N50=845 Kb; Table 1) and was estimated to be 96.9% complete, with only 74 (2.0%) out of 3,640 BUSCO groups missing within the Actinoperygii odb10 database. The Macquarie perch genome was found to be 27.67% repetitive with 33,422 predicted protein-coding genes of which 29,940 were functionally annotated by InterProScan5 with 16,264 having GO annotation.
The 661.43 Mb assembled genome for golden perch (NCBI WGS Project accession VMKM01) was less contiguous, comprising 7,165 scaffolds (scaffold N50=252 Kb; Table 1) and was estimated to be 95.9% complete, missing 85 (2.3%) out of the BUSCO groups above. The golden perch genome was found to be 25.83% repetitive with 36,108 predicted protein-coding genes of which 31,895 were functionally annotated by InterProScan5 with 16,792 having GO annotation.
Sex-linked homozygosity/heterozygosity patterns in DArT-derived SNPs for Macquarie perch and golden perch
We tested 6,939 biallelic DArT-derived SNP loci scored for 93 female and 78 male Macquarie perch, and 5,997 loci scored for 41 female and 25 male golden perch for sex-linked patterns of heterozygosity/homozygosity. Neither species had loci consistent with Y- linkage or XY- (or ZW-) gametologs as defined in Materials and Methods. An order of magnitude more sex-linked loci were found in golden perch compared to Macquarie perch, as follows. Two loci in Macquarie perch and 34 in golden perch were homozygous in males and heterozygous in 10-30% of females, consistent with being old-X-linked, and two loci in Macquarie perch and 14 in golden perch were homozygous in females and heterozygous in 10-30% of males, consistent with bearing recent-Y-specific polymorphism (Table 2, Supplementary Material S2). All putative sex-linked loci aligned to different scaffolds of their respective reference genomes, except two golden perch loci were on the same scaffold VMKM01000203, 226 Kb from each other. Heterozygotes of sex-linked SNPs were present in one sex in multiple populations, except two SNPs per species (indicated in Table 2) had heterozygotes of only one sex but only in a single population.