DOI: 10.5281/zenodo.15801888
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 v6

This update includes re-analyses of exome-capture sequencing data for Kronos EMS mutants generated by Krasileva et al. (2017) and promoter-capture data generated by Zhang et al. (2023). The mutations were identified using the MAPS pipeline as done in the two previous studies. Exome-captureIn this version, a Kronos mutant (Kronos3690) was removed, due to its low quality, and a batch of Kronos mutants that previously included Kronos3690 was re-analyzed. Varient effects were predicted with SnpEff on the v2.1 annotation. Promoter-captureSequencing data produced for 1,556 Kronos mutants were remapped to the Kronos genome v1.1, and EMS-induced mutations were identified using the MAPS pipeline. Varient effects were predicted with SnpEff on the v2.1 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 *.No_RH.maps.substitutions.vcf

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

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

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

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

 

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. 

 

NotesPlease refer to our github to understand how this datasets were produced. Our github is currently being actively updated. Please check additional datasets here: Chromosome-level genome assembly of Triticum turgidum var 'Kronos' additional datasets

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.