Data from: Stepwise evolution of a butterfly supergene via duplication and inversion

Genome_assemblies.tgz (7 files): MB18102_MAT.fasta.gz - Genome assembly of maternal haplotype of individual MB18102, made with Canu. MB18102_PAT.fasta.gz - Genome assembly of paternal haplotype of individual MB18102, made with Canu. SB211_MAT.fasta.gz - Genome assembly of maternal haplotypes from brood SB211, made with Canu. SB211_PAT.fasta.gz - Genome assembly of paternal haplotypes from brood SB211, made with hifiasm. SB211_MAT.hifiasm.fasta.gz - Alternative genome assembly of paternal haplotypes from brood SB211, made with hifiasm. SB211_PAT.canu.fasta.gz - Alternative genome assembly of paternal haplotypes from brood SB211, made with Canu. Dchry2.haplotigs.fasta.gz - Purged haplotigs from Danaus chrysippus assembly Dchry2.2 (Singh et al. 2022). Genome_annotations.tgz (4 files) MB18102_MAT.tidy.gff3 - Genome annotation for MB18102MAT maternal assembly MB18102_PAT.tidy.gff3 - Genome annotation for MB18102PAT paternal assembly SB211_MAT.tidy.gff3 - Genome annotation for SB211MAT maternal assembly SB211_PAT.tidy.gff3 - Genome annotation for SB211PAT paternal assembly Repeat_data.tgz (7 files) Lepidoptera_and_danaus_chrysippus2.2.repeatmasker - Repeat library for Dchry2.2 assembly Dchry2.2.chr15.TE_50kb - Repeat content in 50 kb windows for Dchry2.2 assembly chr15 MB18102MAT.chr15.TE_50kb - Repeat content in 50 kb windows for MB18102MAT maternal assembly chr15 MB18102PAT.chr15.TE_50kb - Repeat content in 50 kb windows for MB18102PAT paternal assembly chr15 SB211PAT.chr15.TE_50kb - Repeat content in 50 kb windows for SB211PAT paternal assembly chr15 SB211MAT.chr15.TE_50kb - Repeat content in 50 kb windows for SB211MAT maternal assembly chr15 DplexMex.chr15.TE_50kb - Repeat content in 50 kb windows for D. plexippus DplexMex assembly chr15 minimap2_alignments.tgz (13 files) DplexMex_Dchry2.2_minimap2.asm20.paf.gz - minimap2 alignment: reference=DplexMex, query=Dchry2.2 DplexMex_Dchry2hap.mm2asm20.paf.gz - minimap2 alignment: reference=DplexMex, query=Dchry2.2HAP haplotigs DplexMex_MB18102MAT.mm2asm20.paf.gz - minimap2 alignment: reference=DplexMex, query=MB18102MAT DplexMex_MB18102PAT.mm2asm20.paf.gz - minimap2 alignment: reference=DplexMex, query=MB18102PAT DplexMex_SB211MAT.mm2asm20.paf.gz - minimap2 alignment: reference=DplexMex, query=SB211MAT DplexMex_SB211PAT.mm2asm20.paf.gz - minimap2 alignment: reference=DplexMex, query=SB211PAT Dchry2.2_MB18102MAT_mm2asm10.paf.gz - minimap2 alignment: reference=Dchry2.2, query=MB18102MAT Dchry2.2_MB18102PAT_mm2asm10.paf.gz - minimap2 alignment: reference=Dchry2.2, query=MB18102PAT Dchry2HAP_MB18102MAT_mm2asm10.paf.gz - minimap2 alignment: reference=Dchry2.2HAP haplotigs, query=MB18102MAT MB18102MAT_SB211PAT.mm2asm10.paf.gz - minimap2 alignment: reference=MB18102MAT, query=SB211PAT SB211PAT_Dchry2.2_mm2asm10.paf.gz - minimap2 alignment: reference=SB211PAT, query=Dchry2.2 SB211MAT_hifiasm_vs_canu.mm2asm10.paf.gz - minimap2 alignment: reference=SB211MAT alternative hifiasm assembly, query=SB211MAT canu assembly SB211PAT_hifiasm_vs_canu.mm2asm10.paf.gz - minimap2 alignment: reference=SB211PAT hifiasm assembly, query=SB211PAT alternative canu assembly Regions_coordinates.tgz (7 files) BC_regions_coordinates_DplexMex_Dplex4.xlsx - Regions 1-4 coordinates in D. plexippus assemblies DplexMex and Dplex4 DplexMex_region_coordinates.tsv - Regions 1-4 coordinates in DplexMex assembly MB18102MAT_region_coordinates.tsv - Regions 1-4 coordinates in MB18102MAT assembly MB18102PAT_region_coordinates.tsv - Regions 1-4 coordinates in MB18102PAT assembly Dchry2.2_region_coordinates.tsv - Regions 1-4 coordinates in Dchry2.2 assembly SB211MAT_region_coordinates.tsv - Regions 1-4 coordinates in SB211MAT assembly SB211PAT_region_coordinates.tsv - Regions 1-4 coordinates in SB211PAT assembly VCF_and_geno_files.tgz (14 files) dan17.BT.DP5GQ20.CDS.vcf.gz - VCF for CDS sites only for 16 Danaus samples and outgroup Tirumala formosa aligned to the Danaus plexippus Dplex4 assembly. dan17.BT.DP5GQ20.4Dsites.geno.gz - Genotypes file for 4-fold degenerate sites only for 16 Danaus samples and outgroup Tirumala formosa aligned to the Danaus plexippus Dplex4 assembly. chry10.BT.Dchry2.2.DP8GQ20.chr15.vcf.gz - VCF for 10 Danaus chrysippus samples aligned to the Dchry2.2 assembly, chr15 only. chry10.BT.Dchry2HAP.DP8GQ20.chr15.vcf.gz - VCF for 10 Danaus chrysippus samples aligned to the Dchry2.2 alternative haplotig, chr15 only. chry10.BT.MB18102MAT.DP8GQ20.chr15.vcf.gz - VCF for 10 Danaus chrysippus samples aligned to the MB18102MAT maternal assembly, chr15 only. chry10.BT.MB18102PAT.DP8GQ20.chr15.vcf.gz - VCF for 10 Danaus chrysippus samples aligned to the MB18102PAT paternal assembly, chr15 only. chry10.BT.SB211MAT.DP8GQ20.chr15.vcf.gz - VCF for 10 Danaus chrysippus samples aligned to the SB211MAT maternal assembly, chr15 only. chry10.BT.SB211PAT.DP8GQ20.chr15.vcf.gz - VCF for 10 Danaus chrysippus samples aligned to the SB211PAT paternal assembly, chr15 only. chry10.BT.Dchry2.2.DP8GQ20.chr15.geno.gz - Genotypes file for 10 Danaus chrysippus samples aligned to the Dchry2.2 assembly, chr15 only. chry10.BT.Dchry2HAP.DP8GQ20.chr15.geno.gz - Genotypes file for 10 Danaus chrysippus samples aligned to the Dchry2.2 alternative haplotig, chr15 only. chry10.BT.MB18102MAT.DP8GQ20.chr15.geno.gz - Genotypes file for 10 Danaus chrysippus samples aligned to the MB18102MAT maternal assembly, chr15 only. chry10.BT.MB18102PAT.DP8GQ20.chr15.geno.gz - Genotypes file for 10 Danaus chrysippus samples aligned to the MB18102PAT paternal assembly, chr15 only. chry10.BT.SB211MAT.DP8GQ20.chr15.geno.gz - Genotypes file for 10 Danaus chrysippus samples aligned to the SB211MAT maternal assembly, chr15 only. chry10.BT.SB211PAT.DP8GQ20.chr15.geno.gz - Genotypes file for 10 Danaus chrysippus samples aligned to the SB211PAT paternal assembly, chr15 only. all_gene_alignments.tgz (5954 files) - sequence alignments for each of 5954 genes (Dplex4 assembly) for 16 Danaus samples and an outgroup Tirumala formosa sample. BC_Region_alignments.tgz (4 files) Region1.1_concat.fasta - Concatenated alignment for genes in Region 1.1 Region1.2_concat.fasta - Concatenated alignment for genes in Region 1.2 Region2_concat.fasta - Concatenated alignment for genes in Region 2 Region4_concat.fasta - Concatenated alignment for genes in Region 4 Diversity_and_divergence_data.tgz (7 files) chry10.BT.Dchry2.2.DP8GQ20.chr15.divStats.w25ksitesMin10k.csv.gz - diversity and divergence measures for 25kb windows for 10 D. chrysippus samples aligned to the Dchry2.2 assembly chr15 chry10.BT.Dchry2HAP.DP8GQ20.chr15.divStats.w25ksitesMin10k.csv.gz - diversity and divergence measures for 25kb windows for 10 D. chrysippus samples aligned to the Dchry2HAP haplotig assembly chr15 chry10.BT.MB18102MAT.DP8GQ20.chr15.divStats.w25ksitesMin10k.csv.gz - diversity and divergence measures for 25kb windows for 10 D. chrysippus samples aligned to the MB18102MAT assembly chr15 chry10.BT.MB18102PAT.DP8GQ20.chr15.divStats.w25ksitesMin10k.csv.gzv - diversity and divergence measures for 25kb windows for 10 D. chrysippus samples aligned to the MB18102PAT assembly chr15 chry10.BT.SB211MAT.DP8GQ20.chr15.divStats.w25ksitesMin10k.csv.gz - diversity and divergence measures for 25kb windows for 10 D. chrysippus samples aligned to the SB211MAT assembly chr15 chry10.BT.SB211PAT.DP8GQ20.chr15.divStats.w25ksitesMin10k.csv.gz - diversity and divergence measures for 25kb windows for 10 D. chrysippus samples aligned to the SB211PAT assembly chr15 dan17.BT.DP5GQ20.4Dsites.divStats.geneWindows.csv.gz - divergence measures for each gene for 16 Danaus samples and one outgroup Tirumala formosa aligned to the Dplex4 assembly Read_depth_data.tgz (7 files) chry10.BT.Dchry2.2.DPstats.w50.csv - Read depth statistics for 50kb windows for 10 D. chrysippus samples aligned to the Dchry2.2 assembly chry10.BT.Dchry2HAP.DPstats.w50.csv - Read depth statistics for 50kb windows for 10 D. chrysippus samples aligned to the Dchry2.2HAP haplotig assembly chry10.BT.MB18102MAT.DPstats.w50.csv - Read depth statistics for 50kb windows for 10 D. chrysippus samples aligned to the MB18102MAT assembly chry10.BT.MB18102PAT.DPstats.w50.csv - Read depth statistics for 50kb windows for 10 D. chrysippus samples aligned to the MB18102PAT assembly chry10.BT.SB211MAT.DPstats.w50.csv - Read depth statistics for 50kb windows for 10 D. chrysippus samples aligned to the SB211MAT assembly chry10.BT.SB211PAT.DPstats.w50.csv - Read depth statistics for 50kb windows for 10 D. chrysippus samples aligned to the SB211PAT assembly dan17.Dplex4.chr7.BT.CDS.allshared.dpstats.geneWindows.csv - Read depth statistics for each gene in Dplex4 chr7 (=chr15 in D. chrysippus) for 16 Danaus samples and an outgroup Tirumala formosa sample IBSrelate_results_NewTrios140202.txt - Relatedness measures for SM18W01, SM18S10 and MB18102