Fasta and tree files used for the analyses

The folder contains the fasta files used to generate the ML phylogenies, the tree files generated, the scaffolds of the four fungal genomes and the fasta files used for recombination analyses. For further information see the "read me" text with explanations for each file

2789_alignments.tar

2789 multiple sequence alignment of protein-coding genes from 7 Neurospora specie

De novo genome assemblies of Neurospora tetrasperma based on Illumina HiSeq reads

This dataset contains 92 de novo genome assemblies of <i>Neurospora tetrasperma</i>, together with one assembly of a <i>N. hispaniola</i> genome (8817) and one assembly of a <i>N. sitophila genome</i> (1135). The genomes were assembled using SOAPdenovo.<br><br>Raw reads have been deposited in the Sequence Read Archive (SRA, https://www.ncbi.nlm.nih.gov/sra/) in BioProjects PRJNA238188 (paired-end reads) and PRJNA239947 (matepair reads for four of the genomes).<br><br>All strains can be ordered from the Fungal Genetics Stock Center (FGSC) at http://www.fgsc.net.<br><br>For further information on the strains and the genome assemblies, please see:<br><br><div> <div>Corcoran, P., Anderson, J.L., Jacobson, D.J., Sun, Y., Ni, P., Lascoux, M., and Johannesson, H. (2016). Introgression maintains the genetic integrity of the mating-type determining chromosome of the fungus <i>Neurospora tetrasperma</i>. Genome Res.</div><div><br></div><div><div> <div><div> <div>Sun, Y., Whittle, C.A., Corcoran, P., and Johannesson, H. (2015). Intron evolution in <i>Neurospora</i>: the role of mutational bias and selection. Genome Res. <i>25</i>, 100–110.</div><div><br></div><div>Sun, Y., Svedberg, J., Hiltunen, M., Corcoran, P., and Johannesson, H. (In press). Large-scale suppression of recombination predates genomic rearrangements in <i>Neurospora tetrasperma</i>.<br></div> </div></div> </div></div> </div

Meunier_etal_Data

This folder contains all data needed to recreate the main figures and tables of the article. Data concern estimation of genetic nuclear ratios of mating types in N.tetrasperma, under different conditions of medium and duration of growth, by qPCR. Measurements of fitness in heterokaryons under different nuclear ratios and in homokaryons are also provided

Meunieretal_Rscripts

This folder contains all scripts in R used to analyze data from the article. Data files to be used with each script are indicated as comments inside the scripts. See README associated with Data for more information

High-quality Neurospora tetrasperma genome assemblies

This dataset contains ten high-quality genome assemblies from ten strains of the fungal genus <i>Neurospora</i>. The genomes are released together with the paper "Large-scale suppression of recombination predates genomic rearrangements in Neurospora tetrasperma" by Sun et al., which is published in Nature Communications (2017).<br><br>Three of the genomes have been assembled using Illumina paired-end and matepair data, which have been scaffolded using optical mapping. The other seven have been assembled using only PacBio data, but have also been error-corrected using Illumina paired-end reads. Raw PacBio reads have been deposited in the Sequence Read Archive (SRA) as part of BioProject PRJNA398702. Raw Illumina reads have also been deposited at SRA in the BioProject PRJNA239947 (matepair reads) and PRJNA239947 (paired-end reads). See Sun et al. for further details.<br><br>Most strains can be ordered from the Fungal Genetics Stock Center at http://www.fgsc.net. Use the FGSC numbers provided below.<br><br>Genomes:<br><br>965A (<i>Neurospora tetrasperma</i>)<br>Technique: Optical mapping + Illumina<br>FGSC number: 10751<br><br>965a (<i>N. tetrasperma</i>)<br>Technique: PacBio<br>FGSC number: 10752<br><br>9033 (<i>N. tetrasperma</i>)<br>Technique: Optical mapping + Illumina<br>FGSC number: 9033<br><br>9034 (<i>N. tetrasperma</i>)<br>Technique: Optical mapping + Illumina<br>FGSC number: 9034<br><br>CJ73 (<i>N. tetrasperma</i>)<br>Technique: PacBio<br>FGSC number: 9045<br><br>CJ74 (<i>N. tetrasperma</i>)<br>Technique: PacBio<br>FGSC number: 9046<br><br>CJ85 (<i>N. tetrasperma</i>)<br>Technique: PacBio<br>FGSC number: 2503<br><br>CJ86 (<i>N. tetrasperma</i>)<br>Technique: PacBio<br>FGSC number: 2504<br><br>8807 (<i>N. intermedia</i>)<br>Technique: PacBio<br>FGSC number: 8807<br><br>W1434 (<i>N. sitophila</i>)<br>Technique: PacBio<br>FGSC number:

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

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'

A possible scenario explaining the evolution of the mating-type (<i>mat</i>) chromosomes in lineages of <i>N. tetrasperma</i>.

<p>A putative scenario for the evolutionary processes leading to the results observed in this study. We speculate that a rearrangement on the <i>mat A</i> chromosome was associated with the evolution of pseudohomothallism in <i>N. tetrasperma</i>. During the subsequent divergence of the <i>N. tetrasperma</i> lineages, additional rearrangements, introgressions and a crossover took place.</p

Concordance factors on the mating-type (<i>mat</i>) chromosome support a post-introgression crossover between the <i>Neurospora tetrasperma</i> L4 <i>mat</i> chromosomes.

<p>The concordance factors are plotted to the left and right of the crossover event described by Menkis et al. (2010) for both the <i>mat A</i> (A and B) and <i>mat a</i> (C and D) chromosomes. Concordance factors are given for the three hypotheses illustrated as clades in the plot, red: <i>N. tetrasperma</i> L9 sister species to <i>N. crassa</i>; blue: <i>N. tetrasperma</i> L4 sister species to <i>N. hispaniola</i>; green: <i>N. tetrasperma</i> monophyletic. The results displayed were calculated with the prior alpha set to 1.</p