Sex comparisons were run on the O_niloticus_UMD1 assembly for two species of tilapia, O. niloticus and O. aureus. The O. niloticus sequence data used in this study was previously described [48 (link)]. The O. aureus individuals used were F1 individuals derived from a stock originally provided by Dr. Gideon Hulata (Institute of Animal Science, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel) and maintained at University of Maryland. These animal procedures were conducted in accordance with University of Maryland IACUC Protocol #R-10-74. A total of 58 O. niloticus XY males, 33 O. niloticus XX females, 22 O. aureus ZZ males and 22 O. aureus WZ females were pooled separately, sheared to ~500 bp on a Covaris shearer, and sequenced on an Illumina HiSeq 2000. The reads from each pool were separately mapped to O_niloticus_UMD1 using BWA mem (v0.7.12). The alignments were sorted and duplicates were marked with Picard (v2.1.0). Alignments were converted into an mpileup file using Samtools (v0.1.18) and subsequently into a sync file using Popoolation2 (v1201) [78 (link)]. Estimates of FST and analyses of sex-patterned variants (SNPs and short deletions that are fixed or nearly fixed in the homogametic sex and in intermediate frequency in the heterogametic sex) were carried out using Sex_SNP_finder_GA.pl (https://github.com/Gammerdinger/sex-SNP-finder ). For the O. niloticus sex comparison, the XX females were set to be the homogametic sex. For the O. aureus comparison, the ZZ males were set to be the homogametic sex.
Full text: Click here