DOI: 10.5061/dryad.xwdbrv1g0
title: Data from: Stepwise evolution of a butterfly supergene via duplication and inversion

description: Supergenes maintain adaptive clusters of alleles in the face of genetic
 mixing. Although usually attributed to inversions, supergenes can be
 complex, and reconstructing the precise processes that led to
 recombination suppression and their timing is challenging. We investigated
 the origin of the BC supergene, which controls variation in warning
 colouration in the African Monarch butterfly, Danaus chrysippus. By
 generating chromosome-scale assemblies for all three alleles, we
 identified multiple structural differences. Most strikingly, we find that
 a region of &gt;1 million bp underwent several segmental duplications
 at least 7.5 million years ago. The resulting duplicated fragments appear
 to have triggered four inversions in surrounding parts of the chromosome,
 resulting in stepwise growth of the region of suppressed recombination.
 Phylogenies for the inversions are incongruent with the species tree, and
 suggest that structural polymorphisms have persisted for at least 4.1
 million years. In addition to the role of duplications in triggering
 inversions, our results suggest a previously undescribed mechanism of
 recombination suppression through independent losses of divergent
 duplicated tracts. Overall, our findings add support for a stepwise model
 of supergene evolution involving a variety of structural changes.
description: PacBio Sequel and Sequel II HiFi
 sequencing Illumina sequencing
 De novo genome assembly Alignment to
 reference genome and genotype calling Whole genome
 alignments and synteny analysis Read depth and copy
 number variation Phylogenetic analysis
description: <strong>Genome_assemblies.tgz</strong> (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).
  
 <strong>Genome_annotations.tgz </strong>(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  
 <strong>Repeat_data.tgz</strong> (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 
  
 <strong>minimap2_alignments.tgz</strong> (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  
 <strong>Regions_coordinates.tgz</strong> (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 
  
 <strong>VCF_and_geno_files.tgz</strong> (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.  
 <strong>all_gene_alignments.tgz</strong> (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 
  
 <strong>Diversity_and_divergence_data.tgz</strong> (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   <strong>Read_depth_data.tgz</strong> (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   <strong>IBSrelate_results_NewTrios140202.txt</strong> - Relatedness measures for SM18W01, SM18S10 and MB18102