SNP data of 556 isolates of the wheat leaf rust fungus, Puccinia triticina from 11 world-wide regions
2019-11-07
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SNP data of 556 isolates of the wheat leaf rust fungus, Puccinia triticina from 11 world-wide regions
Published Date
2019-11-07
Author Contact
Kolmer, James
JKolmer@umn.edu
JKolmer@umn.edu
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Dataset
Genomics Data
Genomics Data
Abstract
This dataset includes SNPs of 556 isolates of the wheat leaf rust fungus, Puccina triticina from 11 worldwide regions that were mapped to the reference genome. This data was used to examine the population structure of Puccinia triticina on a worldwide basis, and to examine the evolutionary relationship between collections from a wheat progenitor, collections from durum wheat, and collections from common wheat. Groups of isolates that were highly related were found in distant continental regions, indicating past and current migration of this important wheat pathogen. Data is being released now in conjunction with publication of a primary research paper that describes this research.
Description
We provide variant calls in VCF and fasta format. Fasta formatted data were used with the deposited python script to calculate the average number of pairwise differences between sequences. GBS SNP calls in Variant Call Format (bgzipped) GBS Haplotype sequence in fasta format (tarballed directory) Python script for calculating average number of pairwise differences using the fasta haplotypes as input. Names dependency file for python script. The excel file gives the virulence/virulence of the same isolates to 20 lines of Thatcher wheat that differ for single leaf rust resistance genes.
Referenced by
Endemic and panglobal genetic groups, and divergence of host-associated forms, in world- wide collections of the wheat leaf rust fungus Puccinia triticina as determined by genotype by sequencing. Heredity 124, 397–409 (2020).
https://doi.org/10.1038/s41437-019-0288-x
https://doi.org/10.1038/s41437-019-0288-x
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Kolmer, James; Herman, Adam; Ordonez, Maria; German, Silvia; Morgounov, Alexy; Pretorius, Zack; Visser, Botma; Anikster, Yehoshoa; Acevedo, Maricelis. (2019). SNP data of 556 isolates of the wheat leaf rust fungus, Puccinia triticina from 11 world-wide regions. Retrieved from the Data Repository for the University of Minnesota (DRUM), https://doi.org/10.13020/0f8c-k469.
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per_locus_fasta.tar.gz
Tarball of per locus fasta files (8,655)
(82.53 MB)
per_locus_rad_pi.py
Pairwise diversity calculator
(2.31 KB)
names4picalc.txt
Names file for pairwise diversity calculator
(22.28 KB)
populations.snps.genome.coordinate.vcf
VCF file of 556 Puccinia triticina isolates from 11 worldwide regions
(107.34 MB)
populations.snps.genome.coordinate.vcf.gz.tbi
Tabix index for VCF
(43.13 KB)
GBS Virulence data - binary (2).xlsx
Virulence data
(55.4 KB)
Readme_208700 AH+JK.txt
Readme Description of the Dataset
(8.39 KB)
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