Fig. 6

Integration of cytogenetic and sequence data, together with a reconstruction of the W-chromosome differentiation in G. affinis. A The acrocentric Z-chromosome shows low abundance of sex-specific SNPs and repeat elements including TEs (green bars), except for the centromere (CEN). Z is comparable to the autosomes, with low green fluorescence intensity (FI) values after in situ hybridization with green fluorescent genomic DNA, whereas oligopainting using a pool of evenly spaced red fluorescent oligonucleotides designed from the male LG 01 assembly (red bars) yielded high FI values on Z, except for CEN. The short arm of the W-chromosome, with high sequence homology to Z and with similar repeat density and red fluorescent paint oligo spacing, showed FI profiles comparable to Z. In contrast, on Wq, the massive accumulation of female-specific SNPs and of repeat elements corresponded with enhanced FI values from green fluorescent genomic DNA and with diminished FI values from red fluorescent Z-oligopaint probe because of higher spacing between adjacent oligos. B Stepwise reconstruction of the inferred most parsimonious pathway of evolutionary W-chromosome differentiation, starting from a pre-W resembling an acrocentric autosome: in the first step, the pre-W becomes structurally rearranged by a centromeric shift concomitant with neocentromere formation. Consequently, recombination is suppressed in the heterozygous Wq segment of the structurally derived proto-W (represented by pale red bars), followed by the accumulation of repeats including TE, and of female-specific SNPs