Supplemental Material for Lichilín et al., 2022

File S2 This file contains large figures representing heatmaps with sample clustering of individual genotypes at SNPs located in the the previously described LG05, LG18 and LG13 sex- determining region in A. burtoni (Böhne et al. 2016; Roberts et al. 2016). Genotypes in blue are heterozygous, in black homozygous reference, and in grey homozygous alternative. HeatmapXYRegionLG05HetBlueNaWhite.pdf Heatmap clustering for genotypes on the previously described XY sex-determining region on LG05. HeatmapXYRegionLG18HetBlueNaWhite.pdf Heatmap clustering for genotypes on the previously described XY sex-determining region on LG18. HeatmapZWRegionHetBlueNaWhite.pdf Heatmap clustering for genotypes on the previously described ZW sex-determining region on LG13. File S3 This file contains large figures investigating sex differences in genome coverage. Female_Assemblies.pdf Coverage 10Kb window visualization for each population and chromosome for female assemblies. Each page shows the mapping coverage for each chromosome within a population. The figures are sorted accordingly to chromosome numbers (columns) first showing the four identified sex chromosomes in A. burtoni LG05/ 14, LG13 and LG18, and then numerically sorted; rows correspond to species. X-axis: chromosomal positions; y-axis: log2 normalized- median coverage. Red lines and dots = female coverage, blue lines and dots = male coverage. yellow lines = windows in the upper 99% quantile of male-female coverage ratio and with normalized-median coverage above 0.25 in females. Male_Assemblies.pdf Coverage 10Kb window visualization for each population and chromosome for male assemblies. Each page shows the mapping coverage for each chromosome within a population. The figures are sorted accordingly to chromosome numbers (columns) first showing the four identified sex chromosomes in A. burtoni LG05/ 14, LG13 and LG18, and then numerically sorted; rows correspond to species. X-axis: chromosomal positions; y-axis: log2 normalized- median coverage. Red lines and dots = female coverage, blue lines and dots = male coverage. yellow lines = windows in the upper 99% quantile of male-female coverage ratio and with normalized-median coverage above 0.25 in males. File S4 This file contains large figures representing sex-specific genome sequence analyses. Female-specific_regions_in_Scaffolds.pdf Scaffolds with female-specific regions of at least 500bp length. Each separate sheet shows the scaffolds found in each population. The right-hand side labels show the assigned scaffold name. Red = female median coverage normalized by overall median depth for the corresponding population across the de novo assembled genome, blue = male median coverage normalized by overall median depth for the corresponding population across the de novo assembled genome. Male-specific_regions_in_Scaffolds.pdf Scaffolds with male-specific regions of at least 500bp length. Each separate sheet shows the scaffolds found in each population. The right-hand side labels show the assigned scaffold name. Red = female median coverage normalized by overall median depth for the corresponding population across the de novo assembled genome, blue = male median coverage normalized by overall median depth for the corresponding population across the de novo assembled genome.

文件S2：本文件包含多张大图，展示了布氏丽鱼（A. burtoni）此前已报道的LG05、LG18及LG13连锁群性别决定区域内，单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点处个体基因型的样本聚类热图（Böhne等，2016；Roberts等，2016）。其中，蓝色代表杂合基因型，黑色代表纯合参考基因型，灰色代表纯合变异基因型。
- HeatmapXYRegionLG05HetBlueNaWhite.pdf：布氏丽鱼LG05连锁群上已报道的XY性别决定区域的基因型聚类热图
- HeatmapXYRegionLG18HetBlueNaWhite.pdf：布氏丽鱼LG18连锁群上已报道的XY性别决定区域的基因型聚类热图
- HeatmapZWRegionHetBlueNaWhite.pdf：布氏丽鱼LG13连锁群上已报道的ZW性别决定区域的基因型聚类热图

文件S3：本文件包含多张用于探究基因组覆盖度性别差异的大图。
1. Female_Assemblies.pdf：雌性基因组组装结果的各群体、各染色体10Kb窗口覆盖度可视化图。每个页面展示单个群体内各染色体的比对覆盖度，图表按染色体编号排序（列方向），优先展示布氏丽鱼已鉴定的4条性染色体：LG05/14、LG13及LG18，随后按数字顺序排列；行方向对应不同物种。横轴为染色体位置，纵轴为log2标准化中位覆盖度。其中，红色线条与点代表雌性覆盖度，蓝色线条与点代表雄性覆盖度，黄色线条代表雄性-雌性覆盖比处于前99%分位数，且雌性标准化中位覆盖度高于0.25的窗口。
2. Male_Assemblies.pdf：雄性基因组组装结果的各群体、各染色体10Kb窗口覆盖度可视化图。每个页面展示单个群体内各染色体的比对覆盖度，图表按染色体编号排序（列方向），优先展示布氏丽鱼已鉴定的4条性染色体：LG05/14、LG13及LG18，随后按数字顺序排列；行方向对应不同物种。横轴为染色体位置，纵轴为log2标准化中位覆盖度。其中，红色线条与点代表雌性覆盖度，蓝色线条与点代表雄性覆盖度，黄色线条代表雄性-雌性覆盖比处于前99%分位数，且雄性标准化中位覆盖度高于0.25的窗口。

文件S4：本文件包含多张用于性别特异性基因组序列分析的大图。
1. Female-specific_regions_in_Scaffolds.pdf：包含长度至少500bp的雌性特异性区域的支架序列（Scaffold）。每个独立工作表展示对应群体中鉴定到的支架序列，右侧标签标注了所分配的支架名称。其中，红色代表雌性中位覆盖度（以对应群体从头组装（de novo assembly）基因组的整体中位深度进行标准化），蓝色代表雄性中位覆盖度（以对应群体从头组装基因组的整体中位深度进行标准化）。
2. Male-specific_regions_in_Scaffolds.pdf：包含长度至少500bp的雄性特异性区域的支架序列（Scaffold）。每个独立工作表展示对应群体中鉴定到的支架序列，右侧标签标注了所分配的支架名称。其中，红色代表雌性中位覆盖度（以对应群体从头组装基因组的整体中位深度进行标准化），蓝色代表雄性中位覆盖度（以对应群体从头组装基因组的整体中位深度进行标准化）。