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Supplemental Material for Lichilín et al., 2022

dataset
posted on 2023-01-10, 15:39 authored by Nicolás Lichilín, Walter Salzburger, Astrid Böhne

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.

History

Article title

No evidence for sex chromosomes in natural populations of the cichlid fish Astatotilapia burtoni