DOI: 10.5281/zenodo.14853918
title: Chromosome-level genome assembly of Triticum turgidum var 'Kronos'

description:  

This data is made available under the Toronto Agreement. 

All of the data listed here is available under the prepublication data sharing principle of the Toronto agreement (1). By using this data, you agree to:



respect the rights of the data producers and contributors to analyze and publish the first global analyses and certain other reserved analyses of this data set in a peer-reviewed publication.

not redistribute, release, or otherwise provide access to the data to anyone outside of the group, until the data has been published & submitted to the public data repositories.

contact the authors to discuss any plans to publish data or analyses that utilize this data to avoid the overlap of any planned analyses.

fully cite the prepublication data along with any applicable versioning details.

understand that this data as accessed is precompetitive and is not patentable in its present state.


This agreement does not expire by time but only upon publication of the first global analysis by the data producers and contributors.(1) Toronto International Data Release Workshop Authors. Prepublication data sharing. Nature 461, 168–170 (2009). https://doi.org/10.1038/461168a

 



If you have questions about the use of this dataset, please contact Ksenia Krasileva: kseniak [at] berkeley.edu


 

Updates in Zenodo v4

This update includes the re-analysis of exome-capture data for Kronos EMS mutants generated by Krasileva et al., 2017. Exome-capture sequencing data produced for 1,440 Kronos mutants were re-mapped to the Kronos reference genome (v1.1). Mutations were called, using the MAPS pipeline and GATK. Varient effects were predicted with SnpEff on the v2 annotation. MAPSThe following four outputs include mutations called by the MAPS pipeline. All files contain high, medium and low-confidence mutations called from uniquely mapped and multi-mapped reads. Each file contains substitutions or indels called from genomic regions with residual hetrogenity (RH_only) or regions without residual hetrogenity (No_RH). The primary output is Kronos_v1.1.Exom-capture.corrected.deduped.10kb_bins.RH.byContig.MI.No_RH.maps.substitutions.snpeff.zip.

Kronos_v1.1.Exom-capture.corrected.deduped.10kb_bins.RH.byContig.MI.No_RH.maps.indels.snpeff.zip

Kronos_v1.1.Exom-capture.corrected.deduped.10kb_bins.RH.byContig.MI.No_RH.maps.substitutions.snpeff.zip

Kronos_v1.1.Exom-capture.corrected.deduped.10kb_bins.RH.byContig.MI.RH_only.maps.indels.snpeff.zip

Kronos_v1.1.Exom-capture.corrected.deduped.10kb_bins.RH.byContig.MI.RH_only.maps.substitutions.snpeff.zip

 

Within vcf files, note the following fields. The primary mutations contain the italicized types below: namely, Substitution, False, High, any indicated threshold, and Unique. Type={Substiution/Indel}: This indicates whether called mutations are substitutions or indels. 

RH={True/False}: This indicates whether called mutations come from regions associated with residual hetrogenity.  

Confidence={High/Medium/Low}: This indicates the confidence level of called mutations.

Threshold=HetMinCov{x}HomMinCov{y}: This indicates parameters used to call the mutations. 

Mapping={Unique/Multi}: This indicates whether called mutations come from uniquely mapped or multi-mapped reads. 

 

GATK

The following zip file contains GATK outputs for all analyzed mutants: Kronos_ems_mutants.gatk.exome.snpeff.vcf.zip. It contains 1,440 vcf files named as {mutant ID}.gatk.exome.snpeff.vcf. No mutations were filtered from initial GATK outputs, and the outputs also contain low-quality mutations. These outputs can be supplementary to the MAPS outputs, if additional mutations need to be explored.  Please access the previous versions of repository to access:Zenovo v1: Chromosome-scale genome assembly v1.0Zenovo v2: Chromosome-scale genome assembly v1.1 & Annotation v1.0Zenovo v3: Annotation v2.0

Acknowledgement

This work has been funded by the United States Department of Agriculture - National Institute for Food and Agriculture Award (2021-67013-35726). Please, feel free to reach out to us regarding this datasets.