Fig. 3

Comparative genomics of LG5 in haplochromine cichlids of Lakes Tanganyika, Malawi and Victoria. In A. burtoni, LG5 has a centric fusion to another chromosome upstream of the blue/red opsin genes [38], probably LG14, here shown on the left site. a LG5 and LG14 show sex association in A. burtoni lab strain. SNP inheritance patterns on LG5 support an XX-XY system on this chromosome in A. burtoni lab strain. LG5 carries a ZZ-ZW SD locus in Lake Malawi cichlids as well as a SD locus in Lake Victoria cichlids. Light blue numbers and boxes correspond to sex-associated SNPs in this study. Gene candidates for sex determination on LG5 are depicted below the corresponding scaffolds of the Nile tilapia. Dark blue boxes and numbers indicate location of male-specific loci. Sex-determining regions of other cichlids are indicated for Lake Malawi in red and Lake Victoria in green. b The plots show the –log10 p-values of genotypes associated with sex plotted against the Nile tilapia chromosomes LG5 and LG14 as higher resolution of Fig. 1. c Gene expression does not show a particular accumulation of sex-biased genes on LG14 or LG5 in A. burtoni lab strain (black dots correspond to significantly differentially expressed genes, grey dots correspond to not differentially expressed genes; values above 0 correspond to overexpression in males, values below 0 to overexpression in females, see Additional file 8: Table S6 for details). The blue box highlights the region with the highest density of Y-linked loci and sex-associated SNPs with the most significant p-values, referred to as SD region