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.
L1 VCF
The 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.gz
L4 VCF
The 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.gz
L5 VCF - scaffold 1 and 2
The 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.gz
L5 VCF - scaffold 3 to 7
The 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.gz
L7 VCF
The 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.gz
L8 VCF - scaffold 1 and 2
The 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.gz
L8 VCF - scaffold 3 to 7
The 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.gz
L9 VCF
The 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.gz
L10 VCF - scaffold 1 and 2
The 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.gz
L10 VCF - scaffold 3 to 7
The 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.gz
indel_vcf.tar
The 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 sequences
The 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.zip
outgroup_alignment
The 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 alignments
The 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.zip
Het loci alignments Fig S8 and Fig S9
Fasta 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