Fig. 4

Sequence differences, distribution of repeat elements, and abundance of sex-specific SNPs on the W- and Z-chromosomes of Gambusia affinis and integration with cytogenomic data. The gaps in the W sequences correspond to stretches of N’s in the published genome assembly [24]. A Sequence difference between W and Z, using W as a reference. B Location of young repeats (with kimura < 1) on W (top panel) and on Z (bottom panel) shows that the W-chromosome, and specifically the long arm Wq, is highly enriched in young repeats compared to Z. C, D The molecular differentiation of the sex chromosomes of G. affinis demonstrates a massive increase in sex-specific single-nucleotide polymorphisms (SNPs) on the W-chromosome compared to autosomes and the Z-chromosome. C Plots showing the number of female- and male-specific SNPs along the 24 chromosomes. D Quantitative analysis of female-specific (magenta) and male-specific (blue) SNPs along female and male LG 01, the W- and Z-chromosome, respectively, using the W-chromosome as a reference