Data from: Introgression maintains the genetic integrity of the sex-determining chromosome of the fungus Neurospora tetrasperma

Corcoran P, Anderson JL, Jacobson DJ, Sun Y, Ni P, Lascoux M, Johannesson H

Date Published: February 17, 2016

DOI: http://dx.doi.org/10.5061/dryad.162mh

 

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Title L1 VCF
Downloaded 23 times
Description 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.
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Title L4 VCF
Downloaded 19 times
Description 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.
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Title L5 VCF - scaffold 1 and 2
Downloaded 6 times
Description 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.
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Title L5 VCF - scaffold 3 to 7
Downloaded 7 times
Description 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.
Download L5_vcf_scaffold_3_to_7.tar.gz (844.7 Mb)
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Title L7 VCF
Downloaded 10 times
Description 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.
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Title L8 VCF - scaffold 1 and 2
Downloaded 7 times
Description 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.
Download L8_vcf_scaffold_1_to_2.tar.gz (554.8 Mb)
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Title L8 VCF - scaffold 3 to 7
Downloaded 5 times
Description 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.
Download L8_vcf_scaffold_3_to_7.tar.gz (781.2 Mb)
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Title L9 VCF
Downloaded 8 times
Description 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.
Download L9_vcf.tar.gz (415.3 Mb)
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Title L10 VCF - scaffold 1 and 2
Downloaded 16 times
Description 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.
Download L10_vcf_scaffold_1_to_2.tar.gz (546.5 Mb)
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Title L10 VCF - scaffold 3 to 7
Downloaded 8 times
Description 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.
Download L10_vcf_scaffold_3_to_7.tar.gz (787.5 Mb)
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Title indel_vcf.tar
Downloaded 7 times
Description 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)
Download indel_vcf.tar.gz (48.01 Mb)
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Title N. tetrasperma consensus sequences
Downloaded 18 times
Description 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'.
Download Ntet_consensus_seqeunces.zip (993.2 Mb)
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Title outgroup_alignment
Downloaded 25 times
Description 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.
Download outgroup_alignment.zip (63.38 Mb)
Download README (556 bytes)
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Title Fig5 alignments
Downloaded 14 times
Description 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.
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Title Het loci alignments Fig S8 and Fig S9
Downloaded 18 times
Description 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).
Download het_loci.zip (16.14 Kb)
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When using this data, please cite the original publication:

Corcoran P, Anderson JL, Jacobson DJ, Sun Y, Ni P, Lascoux M, Johannesson H (2016) Introgression maintains the genetic integrity of the sex-determining chromosome of the fungus Neurospora tetrasperma. Genome Research 26: 486-498. http://dx.doi.org/10.1101/gr.197244.115

Additionally, please cite the Dryad data package:

Corcoran P, Anderson JL, Jacobson DJ, Sun Y, Ni P, Lascoux M, Johannesson H (2016) Data from: Introgression maintains the genetic integrity of the sex-determining chromosome of the fungus Neurospora tetrasperma. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.162mh
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