DOI: 10.5061/dryad.2ngf1vhwj
title: Data from: The role of breakpoint mutations, supergene effects, and ancient nested rearrangements in the evolution of adaptive chromosome inversions in the yellow monkey flower, Mimulus guttatus

description: Large chromosomal inversion polymorphisms are ubiquitous across the
 diversity of diploid organisms and play a large role in the evolution of
 adaptations in those species. Despite their importance, the underlying
 mechanisms by which inversions produce their adaptive phenotypic effects
 and become geographically widespread are still poorly understood. One way
 inversions could cause phenotypic effects is through meiotic recombination
 suppression, which can result in the formation of a supergene containing
 linked adaptive alleles. This supergene hypothesis has been promoted by
 theoreticians, but thus far, no studies have definitively identified
 multiple linked adaptive genes within an inversion. Alternatively,
 according to the breakpoint mutation hypothesis, the inversion mutation
 itself could result in adaptive phenotypic effects if it disrupts genes or
 alters the regulation of nearby genes. Here, we evaluate both of these
 hypotheses using new long-read sequencing-based genomes of the yellow
 monkey flower, Mimulus guttatus. Our results provide support for
 both the supergene and breakpoint mutation hypotheses of adaptive
 inversion evolution and suggest that functional molecular studies will be
 required to definitively test each of these hypotheses. We also identified
 an ancient large inversion nested within a well-established adaptive
 inversion. This finding suggests that the supergene mechanism may occur in
 phases, with an expansion of the region of suppressed recombination
 capturing an increasing number of adaptive loci over time.
description: # **Mimulus guttatus inland annual and coastal perennial genome assembly
 and associated files**
 **[https://doi.org/10.5061/dryad.2ngf1vhwj](https://doi.org/10.5061/dryad.2ngf1vhwj)** These datasets are the result of long read Oxford Nanopore Technologies (ONT) genome assemblies. We assembled genomes for an individual from the inland annual (LMC) and an individual from the coastal perennial ecotype (SWB). We used these genomes to identify chromosomal inversion breakpoint regions, call single nucleotide polymorphisms (SNPs), identify structural variants (SVs), and run differential expression and population genetic analyses on previously published datasets. ## **Description of the data and file structure** ### **Genome assemblies and annotations** 1. Mimulus_guttatus.SWB-S1-2.v1.fa- SWB-S1 genome assembly (pseudochromosomes) 2. Mimulus_guttatus.LMC-L1-2.v1.fa- LMC-L1 genome assembly (pseudochromosomes) 3. Mimulus_guttatus.LMC-L1-2.v1.2.gff - LMC-L1 genome annotation file 4. Mimulus_guttatus.SWB-S1-2.v1.2.gff - SWB-S1 genome annotation file 5. Mimulus_guttatus.LMC-L1-2.v1.2.TEs.gff - LMC-L1 TE annotation file 6. Mimulus_guttatus.SWB-S1-2.v1.2.TEs.gff - SWB-S1 TE annotation file 7. Mimulus_guttatus.LMC-L1-2.v1.2.pseudogenes.gff- LMC-L1 pseudogene annotation file 8. Mimulus_guttatus.SWB-S1-2.v1.2.pseudogenes.gff- SWB-S1 pseudogene annotation file 9. Mimulus_guttatus.LMC-L1-2.v1.2.cds.fa - fasta file with coding sequence. 10. Mimulus_guttatus.SWB-S1-2.v1.2.cds.fa - fasta file with coding sequence. 11. Mimulus_guttatus.LMC-L1-2.v1.2.transcripts.fa - fasta file with transcripts 12. Mimulus_guttatus.SWB-S1-2.v1.2.transcripts.fa - fasta file with transcripts 13. Mimulus_guttatus.LMC-L1-2.v1.2.repeatmasker.gff - repeatmasker annotation file 14. Mimulus_guttatus.SWB-S1-2.v1.2.repeatmasker.gff - repeatmasker annotation file 15. Mimulus_guttatus.LMC-L1-2.v1.2.proteins.fa - protein sequence file 16. Mimulus_guttatus.SWB-S1-2.v1.2.proteins.fa - protein sequence file 17. Mimulus_guttatus.LMC-L1-2.v1.2.suspect-TE-genes.txt - potential TE genes 18. Mimulus_guttatus.SWB-S1-2.v1.2.suspect-TE-genes.txt - potential TE genes 19. Mimulus_guttatus.LMC-L1-2.v1.2.intact-TEs.gff - intact TE annotation file 20. Mimulus_guttatus.SWB-S1-2.v1.2.intact-TEs.gff - intact TE annotation file 21. Mimulus_guttatus.LMC-L1-2.v1.2.functional-annotations.tsv - functional annotation file 22. Mimulus_guttatus.SWB-S1-2.v1.2.functional-annotations.tsv - functional annotation file 23.  Mimulus_guttatus.SWB-S1-2.v1.2.TEs.fa - TE sequence file 24.  Mimulus_guttatus.LMC-L1-2.v1.2.TEs.fa - TE sequence file \_______________________________________________________________\_ ### Variant files #### SNP supplemental files descriptions All files listed in this section were generated by aligning the WGS to the opposite ecotype's reference genome and using the GATK pipeline and filtering to call SNPs.  1. L1_snps_filtered.vcf - Filtered and genotyped SNPs for the inland annual ecotype (LMC) 2. S1_snps_filtered.vcf - FIltered and genotyped SNPs for the coastal perennial ecotype (SWB) 3. L1_filtered.AL.avinput - Filtered and annotated SNPS for the inland annual ecotype (LMC) 4. S1_filtered.AL.avinput - Filtered and annotated SNPS or the inland annual ecotype (LMC) 5. high-impact-L1_synSNV_nothets.csv - A list of high impact mutations for the inland annual ecotype (LMC) 6. high-impact-S1_synSNV_nothets.csv - A list of high impact mutations for the inland annual ecotype (SWB) **Whole genome alignment structural variant calling supplemental files** All files listed in this section were generated by aligning both the SWB-S1 and LMC-L1 assemblies and calling SVs using MUM&co.  1. L1query.pseudo_S1ref.pseudo_mumandco.SVs_notranslocations_nocontractions_noNNNN.zip - L1 structural variants from mumandco where complicated calls (translocations, contractions, and nested SVs), long strings of “NNNN” in insertions and deletions were removed, low quality SVs, and heterozygous SVs were removed. 2. S1query.pseudo_L1ref.pseudo_mumandco.SVs__notranslocations_nocontractions_noNNNN.zip - S1 structural variants from mumandco where complicated calls (translocations, contractions, and nested SVs), long strings of “NNNN” in insertions and deletions were removed, low quality SVs, and heterozygous SVs were removed. 3. L1_*querysnps*_SV_intersected_genes.txt - L1 structural variants intersected with LMC-L1 genes 4. S1_*querysnps*_SV_intersected_genes.txt -  S1 structural variants intersected with SWB-S1 genes 5. S1_pseudogene_intact_gene.csv - A list of SWB-S1 pseudogenes with their corresponding intact gene and the intact genes functional annotation. 6. L1_pseudogene_intact_gene.csv - A list of LMC-L1 pseudogenes with their corresponding intact gene and the intact genes functional annotation. **Read base alignment structural variant calling supplemental files** All files listed in this section were generated by aligning ONT reads from LMC-L1 to the SWB-S1 assembly using minimap2 and vice versa.  1. S1reads_L1ref_minimappbsv.sorted.readgr.vcf - SWB-S1 SVs called using the program pbsv. 2. S1_reads_minimap2_sniffles.vcf - SWB-S1 SVs called using the program sniffles 3. S1_svim_variants.vcf - SWB-S1 SVs called using the program for svim. 4. L1reads_S1ref_minimappbsv.sorted.readgr.vcf - LMC-L1 SVs called using the program pbsv. 5. L1_reads_minimap2_sniffles.vcf - LMC-L1 SVs called using the program pbsv. 6. L1_svim_variants.vcf - LMC-L1 SVs called using the program pbsv **Differential expression supplemental files** All files in this section were generated from the RNAseq data in Gould et al 2018. These files are the output of deseq2 and represent differentially expressed genes.  \** All files below this line are in Supplemental_files-20231211T163038Z-001.zip 1. SWB_aligned_differential_expression_LMC_between_fieldsites.csv - transcripts were aligned to the SWB-S1 genome and differentially expressed between fieldsites within LMC-L1. 2. SWB_aligned_differential_expression_SWB_between_fieldsites.csv - transcripts were aligned to the SWB-S1 genome and differentially expressed between fieldsites within SWB-S1. 3. SWB_aligned_differential_expression_genotype_by_fieldsites.csv - transcripts were aligned to the SWB-S1 genome and differentially expressed G x E. 4. SWB_aligned_differential_expression_between_genotypes.csv - transcripts were aligned to the SWB-S1 genome and differentially expressed between genotypes. 5. LMC_aligned_differential_expression_LMC_between_fieldsites.csv - transcripts were aligned to the LMC-L1  genome and differentially expressed between fieldsites within LMC-L1. 6. LMC_aligned_differential_expression_SWB_between_fieldsites.csv - transcripts were aligned to the LMC-L1 genome and differentially expressed between fieldsites within SWB-S1. 7. LMC_aligned_differential_expression_genotype_by_fieldsites.csv - transcripts were aligned to the LMC-L1 genome and differentially expressed G x E. 8. LMC_aligned_differential_expression_between_genotypes.csv - transcripts were aligned to the LMC-L1 genome and differentially expressed between genotypes. **Pool sequencing supplemental files** All files listed in this section were generated from the pool sequencing data in Gould et al 2017. These files are the top 1% of the *G *statistic and Fst, and π ratio and also the bottom 1% of π ratio.  1. S1_top1_pi_intersect_descriptions_all.txt - the top 1% of pi ratio windows falling within genes. This file was aligned to the SWB genome. 2. S1_bottom1_pi_intersect_descriptions_all.txt - the bottom 1% of pi ratio windows falling within genes. This file was aligned to the SWB genome. 3. S1_top1_FST_descriptions.txt - the top 1% of FST windows falling within genes. This file was aligned to the SWB genome. 4. S1_top1_gstat_descriptions.txt - the top 1% of *G *statistic windows falling within genes. This file was aligned to the SWB genome. 5. L1_top1_pi_intersect_descriptions_all.txt - the top 1% of pi ratio windows falling within genes. This file was aligned to the LMC genome. 6. L1_bottom1_pi_intersect_descriptions_all.txt - the bottom 1% of pi ratio windows falling within genes. This file was aligned to the LMC genome. 7. L1_top1_FST_descriptions.txt - the top 1% of FST windows falling within genes. This file was aligned to theLMC genome. 8. L1_top1_gstat_descriptions.txt -  the top 1% of *G *statistic windows falling within genes. This file was aligned to the LMC genome. **GENESPACE output files for CNVs, PAVs, tandem duplicates, and synthetic and non syntenic genes** All files listed in this section were generated using orthology constrained synteny (GENESPACE) and further manipulated using custom scripts. 1. SWB_SWB_dotplots.pdf - comparison of SWB and SWB synteny 2. LMC_LMC_dotplots.pdf - comparison of LMC and LMC synteny 3. LMC_SWB_dotplots.pdf - comparison of LMC and SWB synteny 4. LMC_LMC_synHits.txt.gz - a list of LMC syntenic hits 5. LMC_SWB_synHits.txt.gz - a list of LMC and SWB syntenic hits 6. SWB_SWB_synHits.txt.gz - a list of SWB syntenic hits 7. syntenicBlocks.txt.gz - a list of syntenic blocks for both LMC and SWB 8. tandem_arrays_L1S1.txt - a list of tandem arrays between LMC and SWB 9. S1_syntelogs.txt - a list of SWB syntelogs 10. L1_syntelogs.txt - a list of LMC syntelogs 11. S1_nonsyntenic.txt - a list of non syntenic genes in SWB 12. L1_nonsyntenic.txt - a list of non syntenic genes in LMC 13. L1_S1_different_copy_numbers.txt - a list of genes with different copy numbers between LMC and SWB 14. L1_1x1_syntelogs.txt - filtered LMC syntelogs 15. S1*_*1x1_syntelogs.txt - filtered SWB syntelogs 16. absent_S1_present_L1.txt - a list of genes present in LMC but not SWB. 17. absent_L1_present_S1.txt - a list of genes present in SWB but not LMC ## Sharing/Access information Links to other publicly accessible locations of the data: * Raw ONT data - NCBI Sequence Read Archive under project identifier PRJNA1047892 – accessions SAMN38597945 (LMC-L1) and SAMN38597946 (SWB-S1) * Raw RNA sequencing - NCBI Sequence Read Archive under project identifier PRJNA1054563. * LMC and SWB Genome assemblies - Can be found on CoGe as well as this repository ## Code/Software Code for genome assembly can be found at [https://github.com/niederhuth/mimulus-assembly](https://github.com/niederhuth/mimulus-assembly) and code for calling structural variants and SNPs, reanalysis of pooled sequencing and RNAseq, and figures can be found at [https://github.com/Kollarlm/Breakpoint-mutations-supergene-effects-and-ancient-nested-rearrangements-in-yellow-monkey-flower.git](https://github.com/Kollarlm/Breakpoint-mutations-supergene-effects-and-ancient-nested-rearrangements-in-yellow-monkey-flower.git).