Data from: The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies

The dataset contains intermediate output files required to reproduce the figures in the main text and Supporting Material of Willink et al. 2023. The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies.

FILE OVERVIEW:

1. Morph-specific assemblies
    A. File names: Afem_1354_ragtag.fasta.gz, Ifem_1049_ragtag.fa.gz, Ofem_0081_ragtag.fa.gz, O054_Shasta_run2.PMDV.HAP1.purged.fasta.gz, A059_Shasta_run1.PMDV.HAP1.purged.fa.gz
    B. Description: genome assemblies for different morphs of Ischnura elegans (Afem_1354, Ifem_1049, and Ofem_0081) and Ischnura senegalensis (A059 and O054), generated in this study from long-read Nanopore data using Shasta v 0.7.0 (https://github.com/paoloshasta/shasta).

2. Assembly statistics
    A. File names: Assembly_statistics.csv, Assembly_statistics_sen.csv
    B. Description: Completeness and quality metrics for de novo genome assemblies of I. elegans and I. senegalensis female morphs. See Fig. S1-S2.

3. Repetitive content annotation
    A. File names: A1354_ragtag_RED.bed.repeats.bed.gz, Afem_Shasta1_polished_ragtag_UPPER.fa.out.gz, Ifem_Shasta2_polished_ragtag_UPPER.fa.out.gz, ioIscEleg1.1.primary_UPPER.fa.out.gz, ToL_RED.repeats.bed.gz
    B. Description: Annotation of repetitive sequences in morph-specific assemblies. All morph assemblies (A, I and Darwin Tree of Life assemblies) were annotated using RepeatModeler v 2.0.1 and RepeatMasker v 1.0.93 (http://www.repeatmasker.org). The A morph and  DToL assemblies were additionally annotated using Red v 0.0.1 (https://github.com/BioinformaticsToolsmith/Red). RepeatMasker annotations were then used to estimate TE coverage. See Extended Data Fig. 4 and Fig. S7.

4. GWAS output
    A. File names: A1354_ragtag_AvI.assoc_filtered.txt.gz, A1354_ragtag_AvO.assoc_filtered.txt.gz, A1354_ragtag_IvO.assoc_filtered.txt.gz, ToL_AvI.assoc_filtered.txt.gz, ToL_AvO.assoc_filtered.txt.gz, ToL_IvO.assoc_filtered.txt.gz
    B. Description: filtered SNPs in pairwise association tests between morphs (n = 19 resequencing samples per morph) of I. elegans. Analyses were conducted in PLINK v 1.9 (http://pngu.mgh.harvard.edu/purcell/plink/), using either the A morph assembly (Fig. 2a-b), or the Darwin Tree of Life (DToL) reference assembly (Extended Data Figure 8a-b) as mapping reference.

5. Population statistics
    A. File names: Afem_pixy_30K_fst.txt.gz, A1354_30kb.Tajima.D.gz, Afem_pi_30K_pi.txt.gz, ToL_30K_fst.txt.gz, ToL_30kb.Tajima.D.gz, ToL_30K_onepop_pi.txt.gz
    B. Description: Genetic differentiation (fst) between morphs, Tajima's D statistics, and nucleotide diversity across 30 kb windows of the I. elegans genome. Population statistics were computed using either the A morph assembly (Fig. 2c-e), or the DToL reference assembly (Extended Data Figure 8c-e) as mapping reference.

6. k-mer based GWAS
    A. File names: AvI_kmers.fa.gz, AvO_kmers.fa.gz, OvAI_kmers.fa.gz, AvI_kmers.fa_v_A1354_Shasta_run1_table.tsv.gz, AvO_kmers.fa_v_A1354_Shasta_run1_table.tsv.gz, OvAI_kmers.fa_v_A1354_Shasta_run1_table.tsv.gz, OvAI_kmers.fa_v_Ifem_1049_ragtag_table.tsv.gz
    B. Description: List of significant k-mers (in fasta format) in three k-mer based association analyses (n = 19 resequencing samples per morph) between morphs of I. elegans. Significant k-mers were then mapped to morph-specific assemblies using Blast v 2.22.28 (https://blast.ncbi.nlm.nih.gov/Blast.cgi) for short sequences. We include mapping results shown in Fig. 3a-b.

7. Read-depth coverage
    A. File names: reseq_coverage_norepeat_500_window.bed.gz, nano_coverage_norepeat_500_window.bed.gz, Ifem_nano_coverage_norepeat_500_window.bed.gz, Ifem_reseq_coverage_norepeat_500_window_15Mb.bed.gz, poolseq_coverage_norepeat_500_window.bed.gz, morph_coverage_norepeat_diff_500.tsv.gz, SwD_popmap
    B. Description: Read depth coverage of the morph locus and a 15 mb region used to estimate baseline read depths. 19 Illumina resequencing samples, and one long-read Nanopore sample of each morph of I. elegans were mapped to both the A and I assemblies to estimate read depth. Two poolseq samples (each pool consisting of 30 females of each morph) of I. senegalensis were mapped to the A assembly of I. elegans to estimate read depth. Read depth was estimated in mosdepth v 0.2.8 (https://github.com/brentp/mosdepth) across 500 bp windows after filtering windows with more than 10% repetitive content. For poolseq samples, the difference in coverage values between the A and O pools was computed across the entire genome. Sample information for resequencing samples is recorded in the file SwD_popmap. See Fig. 3c-d, 5b, and S8.

8. Assembly alignment
    A. File names: nucmer_aln_Ifem_1049_ragtag_Afem_1354_ragtag.qr1_filter.reformat.coords.gz, nucmer_aln_Ofem_0081_ragtag_Afem_1354_ragtag.qr1_filter.reformat.coords.gz, nucmer_aln_Afem_Isen_Afem_Iele.qr1_filter.reformat.coords.gz, nucmer_aln_Ofem_Isen_Afem_Iele.qr1_filter.reformat.coords.gz, karyotype_AI_RagTag.csv, karyotype_AO_RagTag.csv, karyotype_AIsen_AIele.cs, karyotype_OIsen_AIele.csv
    B. Description: Assembly alignments using nucmer v 4.0.0 (https://github.com/mummer4/mummer) and contig synteny for plotting using RIdeogram v 0.2.2 (https://cran.r-project.org/web/packages/RIdeogram/vignettes/RIdeogram.html) in R v 4.2.2 (https://www.r-project.org/). The A morph assembly of I. elegans was aligned to the I and O morph assemblies of I. elegans and to the A and O-like assemblies of I. senegalensis. See Fig. 4a, 5c.

9. Genotyping the Darwin Tree of Life assembly
    A. File names: nucmer_aln_Afem_ragtag_ToL-haplotigs.qr1_filter.reformat.coords.gz, nucmer_aln_Afem_ragtag_ToL-primary.qr1_filter.reformat.coords.gz, ToL_500_norepeat.regions.bed.gz, karyotype_AToL_13_unloc_RagTag.csv, karyotype_AToL_RagTag_haplotigs.csv
    B. Description: To genotype the DToL reference assembly of I. elegans, we estimated read-depth coverage of the DToL long-read Pacbio data mapped to the A morph assembly of I. elegans generated in this study, and aligned the A morph assembly to both the primary DToL assembly and to the purged haplotigs. Read depth was estimated in mosdepth v 0.2.8 (https://github.com/brentp/mosdepth) and assembly alignments were conducted using nucmer v 4.0.0 (https://github.com/mummer4/mummer). See Fig. S3.

10. SV calling
    A. File names: A_to_A.bam, A_to_A.bam.bai, A_to_I.bam, A_to_I.bam.bai, A_to_O.bam, A_to_O.bam.bai, A_to_ToL_2mb.bam, A_to_ToL_2mb.bam.bai, I_to_A.bam, I_to_A.bam.bai, I_to_I.bam, I_to_I.bam.bai, I_to_O.bam, I_to_O.bam.bai, I_to_ToL_2mb.bam, I_to_ToL_2mb.bam.bai, O_to_A.bam, O_to_A.bam.bai, O_to_I.bam, O_to_I.bam.bai, O_to_O.bam, O_to_O.bam.bai, O_to_ToL_2mb.bam, O_to_ToL_2mb.bam.bai
    B. Description: mergede alignements of resequencing samples (n = 19 per morph) to alternative reference assemblies (A, I, O, and DToL) for I. elegans. The alignments have been filtered by quality and to contain only the unlocalized scaffold 2 of chromosome 13, which includes the morph locus. These files were used to call morph-specific structural variants using samplot v 1.3.0 (https://github.com/ryanlayer/samplot). See Extended Data Figs 2, 7, and Fig. S5-S6.

11. Mapping of inversion breakpoint reads
    A. File names: AvO_3K.tsv.gz, AvO_22K.tsv.gz, AvO_sen_3K.tsv.gz, AvO_sen_22K.tsv.gz, IvO_3K.tsv.gz
    B. Description: Signatures of an inversion with breakpoints at ~ 3 kb and ~ 22 kb of the unlocalized scaffold 2 of chromosome 13 on the O assembly were found in A and I resequencing samples of I. elegans and in poolseq samples of A females of I. senegalensis. We queried the reads mapping to the inversion breakpoints and then tabulated their mapping locations of the A morph assembly of I. elegans (Fig. 6 and Extended Data Fig. 3, 7b-c). For the first inversion breakpoint, we also mapped reads on the I morph assembly of I. elegans (Fig. S12).

12. Evidence of translocation in I
    A. File names: Ifem_nano_SUPER_13_unloc_2.bam, Ifem_nano_SUPER_13_unloc_2.bam.bai
    B. Description: Long-read Nanopore data of a I morph female of I. elegans mapped to the A morph of I. elegans and filtered to contain the entire unlocalized scaffold 2 of chromosome 13. Read mapping was conducted in minimap2 v 2.22-r1110 (https://github.com/lh3/minimap2) and used to identify a translocation signature in the I morph, relative to the A morph of I. elegans. See Extended Data Fig. 6.

13. PCA output
    A. File names: A1354_all.eigenval, A1354_all.eigenvec, I1049_all.eigenval, I1049_all.eigenvec
    B. Description: Eigenvectors and eigenvalues of PCA analyses of population structure between morphs of I. elegans. PCA analysis were conducted on morph locus, using either the A morph or the I morph assembly as mapping reference in PLINK v 1.9 (http://pngu.mgh.harvard.edu/purcell/plink/). See Fig. S4.

14. Linkage disequilibrium
    A. File names: A1354_SUPER_1_allr.ld.gz, A1354_SUPER_2_allr.ld.gz, A1354_SUPER_3_allr.ld.gz, A1354_SUPER_4_allr.ld.gz, A1354_SUPER_5_allr.ld.gz, A1354_SUPER_6_allr.ld.gz, A1354_SUPER_7_allr.ld.gz, A1354_SUPER_8_allr.ld.gz, A1354_SUPER_9_allr.ld.gz, A1354_SUPER_10_allr.ld.gz, A1354_SUPER_11_allr.ld.gz, A1354_SUPER_12_allr.ld.gz, A1354_SUPER_13_allr.ld.gz, A1354_SUPER_13_unloc_1_allr.ld.gz, A1354_SUPER_13_unloc_2_allr.ld.gz, A1354_SUPER_13_unloc_3_allr.ld.gz, A1354_SUPER_13_unloc_4_allr.ld.gz, A1354_SUPER_X_allr.ld.gz
    B. Description: Estimates of recombination rate (R2) between SNPs across the first 15 mb of each chromosome and unlocalized segments of chromosome 13 of I. elegans. Recombination rates were estimated based on 57 resequencing samples and using the A morph assembly as mapping reference in PLINK v 1.9 (http://pngu.mgh.harvard.edu/purcell/plink/). See Extended Data Fig. 5.

15. Gene annotations
    A. File names: Afem_all_ragtag.gtf.gz, Afem_all_transcripts.transdecoder.genome.gff3.gz, Isen.gtf.gz
    B. Description: Annotation of the A morph assembly of I. elegans using RNAseq data to assemble transcripts de novo for I. elengans and I. senegalensis in Stringtie v 2.1.4 (https://ccb.jhu.edu/software/stringtie/). Peptide sequences for the I. elegans transcripts were then predicted using Transdecoder v 5.5.0 (https://github.com/TransDecoder/TransDecoder).

16. Gene annotations in the morph locus
    A. File names: gene_models_shared_trancripts_simple.csv, gene_models_shared_trancripts_simple_I.csv
    B. Description: locations of exon features for genes in the morphs locus and expressed in at least one adult sample of both I. elegans and I. senegalensis. Locations are given for the A and I assemblies. See Fig. 6 and S12.

17. Gene expression
    A. File names: DToL_gene_count_matrix.csv.gz, DToL_transcript_count_matrix.csv.gz, gene_count_matrix.csv.gz, transcript_count_matrix.csv.gz, Isen_gene_count_matrix.csv.gz, Isen_transcript_count_matrix.csv.gz, Iele_phenodata.csv, Isen_phenodata.csv
    B. Description: Sample information (phenodata), gene and transcript count matrices for gene expression analysis. For I. elegans, gene expression was quantified on thoracic tissue of six adult females of each morph and six adult males (three sexually mature and three sexually immature in each group). Reads were mapped to both the A morph assembly and the DToL reference assembly. For I. senegalensis, we used previously published data (NCBI BioProject PRJDB11387) from different tissues of adult females of each morph and males (one upon emergence and one two days after emergence for each group) mapped to the A morph assembly. Gene and transcript counts were generated using Stringtie v 2.1.4 (https://ccb.jhu.edu/software/stringtie/). See Fig. 6, S9-S11, S13.

18. SNPs in the morph locus
    A. File names: A1354-ragtag-allsites-candidate_gene_cds.vcf.gz, A1354-ragtag-allsites-candidate_gene_cds.vcf.gz.tbi, vcf_popmap
    B. Description: SNPs in 57 resequencing samples across coding sequences of the morph locus of I. elegans. The A morph assembly was used as mapping reference. Sample information for resequencing samples is recorded in the file vcf_popmap. See Fig. S14a.

19. Domains and orthologues of Gastrula zinc-finger transcription factor in the morph locus
    A. File names: GZnf_domain_annot.csv, GZnF_orthologue.tre, GZnf_orthologue_annot.txt
    B. Description: Functional domains were annotated using InterProScan (https://www.ebi.ac.uk/interpro/). The gene orthologue tree was inferred using OrthoFinder v 2.5.2 (https://github.com/davidemms/OrthoFinder). See Fig. S14.