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Published May 1, 2024 | Version v1
Dataset Open

Wheat Enhanced Disease Resistance EMS-Mutants Include Lesion-mimics With Adult Plant Resistance to Stripe Rust

Creators

  • 1. ROR icon University of California, Berkeley
  • 2. ROR icon University of California, Davis
  • 3. ROR icon Sainsbury Laboratory
  • 4. University of Maryland
  • 5. ROR icon Washington State University
  • 6. ROR icon North Dakota State University
  • 7. ROR icon Agricultural Research Service
  • 8. ROR icon Oklahoma State University
  • 9. ROR icon Oregon State University

Description

The datasets for 'Wheat Enhanced Disease Resistance EMS-Mutants Include Lesion-mimics With Adult Plant Resistance to Stripe Rust'.

 

Main datasets

  • combined.mapspart2.Lib20HetMinPer15HetMinCovVariableHomMinCovVariable.reformatted.corrected.10kb_bins.RH.byContig.MI.No_RH.maps.vcf
  • combined.mapspart2.Lib20HetMinPer15HetMinCovVariableHomMinCovVariable.reformatted.corrected.10kb_bins.RH.byContig.MI.No_RH.maps.allGenes.snpeff.vcf
  • combined.mapspart2.Lib20HetMinPer15HetMinCovVariableHomMinCovVariable.reformatted.corrected.10kb_bins.RH.byContig.MI.No_RH.maps.highConf.snpeff.vcf

These three files contain substitutions called from the EMS mutant lines included in the study, as well as a non-mutagenized control line. For each line, different HetMinCov and HomMinCov were set to maximize the number of EMS-type mutations, while retaining % EMS mutations ≥ 98%. The selected parameters are recorded in our publication. The mutation effects were predicted with snpeff for either 69,909 high-confidence genes or both high- and low-confidence genes. The mutations that stemmed from residual heterogeneity were removed.

 

Supplemental datasets

  • combined.mapspart2.Lib20HetMinPer15HetMinCovVariableHomMinCovVariable.reformatted.corrected.10kb_bins.RH.byContig.MI.RH_only.maps.vcf
  • combined.mapspart2.Lib20HetMinPer15HetMinCovVariableHomMinCovVariable.reformatted.corrected.10kb_bins.RH.byContig.MI.RH_only.maps.allGenes.snpeff.vcf
  • combined.mapspart2.Lib20HetMinPer15HetMinCovVariableHomMinCovVariable.reformatted.corrected.10kb_bins.RH.byContig.MI.RH_only.maps.highConf.snpeff.vc

These three files are produced in the same manner as the main datasets but contain substitutions that originate from residual heterogeneity. 

 

  • Variable_HetMinCov_HomMinCov_no_RH.zip 

This folder contains the raw output files of called mutations with varying HetMinCov and HomMinCov parameters, excluding mutations from residual heterogeneity.

  • Variable_HetMinCov_HomMinCov_RH.zip

This folder contains the raw output files of called mutations with varying HetMinCov and HomMinCov parameters for mutations related to residual heterogeneity.

  • Orthogroups.zip
  • Orthogroups-known_genes.zip

This folder contains outputs from OrthoFinder that we used to infer orthology between known genes of interest and Kronos genes. Orthogroups.zip does not include known genes, while Orthogroups-known_genes.zip does. 

 

 

 

 

Files

Orthogroups-known_genes.zip

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