DOI: 10.5061/dryad.162mh
title: Data from: Introgression maintains the genetic integrity of the sex-determining chromosome of the fungus Neurospora tetrasperma

description: Genome evolution is driven by a complex interplay of factors, including
 selection, recombination, and introgression. The regions determining
 sexual identity are particularly dynamic parts of eukaryotic genomes that
 are prone to molecular degeneration associated with suppressed
 recombination. In the fungus Neurospora tetrasperma, it has been proposed
 that this molecular degeneration is counteracted by the introgression of
 non-degenerated DNA from closely related species. In this study, we used
 comparative and population genomic analyses of variation among 92 genomes
 from eight phylogenetically and reproductively isolated lineages of N.
 tetrasperma, and its three closest relatives, to investigate the factors
 shaping the evolutionary history of the genomes. We found that suppressed
 recombination extends across at least 6 Mbp (~63%) of the mating-type
 (mat) chromosome in N. tetrasperma, and is associated with decreased
 genetic diversity, which is likely the result primarily of selection at
 linked sites. Furthermore, analyses of molecular evolution revealed an
 increased mutational load in this region, relative to recombining regions.
 However, comparative genomic and phylogenetic analyses indicate that the
 mat chromosomes are temporarily regenerated via introgression from sister
 species; six out of eight lineages show introgression into one of their
 mat chromosomes, with at least three other Neurospora species acting as
 donors. The introgressed tracts have been driven to fixation in lineages,
 suggesting that they confer an adaptive advantage in natural populations,
 and our analyses support the presence of selective sweeps in at least one
 of the lineages. Thus, these data strongly support the previously
 hypothesized role of introgression as a mechanism for the maintenance of
 mating-type determining chromosomal regions.
description: L1 VCFThe L1_vcf.tar.gz folder
 contains the compressed all-sites VCF file for L1 and the index file for
 that VCF file contains. The all-sites VCF file was generated using GATK
 UnifiedGenotyper, as described in the paper.L1_vcf.tar.gzL4 VCFThe L4_vcf.tar.gz folder contains the compressed all-sites VCF file for L4 and the index file for that VCF file. The all-sites VCF file was generated using GATK UnifiedGenotyper, as described in the paper.L4_vcf.tar.gzL5 VCF - scaffold 1 and 2The L5_vcf_scaffold_1_to_2.tar.gz folder contains the compressed all-sites VCF file for L5 and the index file for that VCF file. This file contains scaffold 1 and 2. The all-sites VCF file was generated using GATK UnifiedGenotyper, as described in the paper.L5_vcf_scaffold_1_to_2.tar.gzL5 VCF - scaffold 3 to 7The L5_vcf_scaffold_3_to_7.tar.gz folder contains the compressed all-sites VCF file for L5 and the index file for that VCF file. This file contains scaffold 3 to 7. The all-sites VCF file was generated using GATK UnifiedGenotyper, as described in the paper.L5_vcf_scaffold_3_to_7.tar.gzL7 VCFThe L7_vcf.tar.gz folder contains the compressed all-sites VCF file for L7 and the index file for that VCF file. The all-sites VCF file was generated using GATK UnifiedGenotyper, as described in the paper.L7_vcf.tar.gzL8 VCF - scaffold 1 and 2The L8_vcf_scaffold_1_to_2.tar.gz folder contains the compressed all-sites VCF file for L8 and the index file for that VCF file. This file contains scaffold 1 and 2. The all-sites VCF file was generated using GATK UnifiedGenotyper, as described in the paper.L8_vcf_scaffold_1_to_2.tar.gzL8 VCF - scaffold 3 to 7The L8_vcf_scaffold_3_to_7.tar.gz folder contains the compressed all-sites VCF file for L8 and the index file for that VCF file. This file contains scaffold 3 to 7. The all-sites VCF file was generated using GATK UnifiedGenotyper, as described in the paper.L8_vcf_scaffold_3_to_7.tar.gzL9 VCFThe L9_vcf.tar.gz folder contains the compressed all-sites VCF file for L9 and the index file for that VCF file. The all-sites VCF file was generated using GATK UnifiedGenotyper, as described in the paper.L9_vcf.tar.gzL10 VCF - scaffold 1 and 2The L10_vcf_scaffold_1_to_2.tar.gz folder contains the compressed all-sites VCF file for L10 and the index file for that VCF file. This file contains scaffold 1 and 2. The all-sites VCF file was generated using GATK UnifiedGenotyper, as described in the paper.L10_vcf_scaffold_1_to_2.tar.gzL10 VCF - scaffold 3 to 7The L10_vcf_scaffold_3_to_7.tar.gz folder contains the compressed all-sites VCF file for L10 and the index file for that VCF file. This file contains scaffold 3 to 7. The all-sites VCF file was generated using GATK UnifiedGenotyper, as described in the paper.L10_vcf_scaffold_3_to_7.tar.gzindel_vcf.tarThe indel_vcf.tar.gz folder contains the filtered indel VCF files produced by GATK using the tool UnifiedGenotyper. There is a VCF file for each lineage (L1, L4, L5, L7, L8, L9 and L10). The VCF files are named according to the Lineages (e.g., the VCF file called L5_filtered_indel_final.recode.vcf contains the indels for L5)N. tetrasperma consensus sequencesThe consensus_sequences folder contains the consensus sequences for 92 strains of N. tetrasperma, in fasta format, generated from the all-sites vcf files, as described in the paper . Each file contains the consensus sequence for the seven largest scaffolds in the reference 2509 mat a genome and coordinates follow the 2509 reference genome. Each file is named using the homokaryon id listed in Supplementary Table 1 of the paper. The consensus sequences have had repetitive regions masked to 'N'.Ntet_consensus_seqeunces.zipoutgroup_alignmentThe outgroup_alignment folder contains the alignment of the heterothallic species described in the paper in fasta format for each chromosome. The coordinates follow the 2509 N. tetrasperma mat a reference genome.Fig5 alignmentsThe Fig5_alignments folder contains a fasta format alignment gene alignments of the 6 SR and 2 PAR genes listed in Supplementary Table 12 and used in the reconstruction of the Fig5 phylogenetic trees.Fig5_alignments.zipHet loci alignments Fig S8 and Fig S9Fasta format mulitple sequence alignments for het-6 and het-c used to construct the phylogenetic trees for het-6 (Fig S8) and het-c (Fig S9).het_loci.zip