Data
Zymoseptoria tritici, wheat pathogen¶
Zymoseptoria tritici is a pathogen responsible for Septoria leaf blotch in wheat. The genome of Z.tritici is haploid, 40 Mb long and contains 21 chromosomes, 8 of which are accessory (14-21). Several complete genomes are available and have been used to explore the sequence specificity of diverse populations sampled worldwide. Here we propose to work with 8 genomes previously analysed as part of the establishment of a gene pangenome in the Badet et al, 2020 study. We will focus on chromosome 5, which shows a pattern of presence/absence of a group of genes. The strain TN09 contains a specific gene cluster (Indole Metabolism) with 9 genes (jg9858 to jg9866).
List of genomes and associated files:
| Strain | Genome | Genes | TEs |
|---|---|---|---|
| Aus01 | Aus01.chr_5.fa.gz | Aus01.chr_5.genes.gff.gz | Aus01.chr_5.TE.gff.gz |
| IPO323 | IPO323.chr_5.fa.gz | IPO323.chr_5.genes.gff.gz | IPO323.chr_5.TE.gff.gz |
| ST99CH_1A5 | ST99CH_1A5.chr_5.fa.gz | ST99CH_1A5.chr_5.genes.gff.gz | ST99CH_1A5.chr_5.TE.gff.gz |
| ST99CH_1E4 | ST99CH_1E4.chr_5.fa.gz | ST99CH_1E4.chr_5.genes.gff.gz | ST99CH_1E4.chr_5.TE.gff.gz |
| ST99CH_3D1 | ST99CH_3D1.chr_5.fa.gz | ST99CH_3D1.chr_5.genes.gff.gz | ST99CH_3D1.chr_5.TE.gff.gz |
| ST99CH_3D7 | ST99CH_3D7.chr_5.fa.gz | ST99CH_3D7.chr_5.genes.gff.gz | ST99CH_3D7.chr_5.TE.gff.gz |
| TN09 | TN09.chr_5.fa.gz | TN09.chr_5.genes.gff.gz | TN09.chr_5.TE.gff.gz |
| YEQ92 | YEQ92.chr_5.fa.gz | YEQ92.chr_5.genes.gff.gz | YEQ92.chr_5.TE.gff.gz |
We will also work with strains from field populations of Z.tritici. These strains were sequenced in short-reads. The data are available under the Bioproject: PRJNA777581 We perform a selection of subset from several runs for this tutorial:
- SRR16762562
- ...
Download all data at once:
wget https://genotoul-bioinfo.pages.mia.inra.fr/pangenome_hackathon/data/ztritici.tar
# if you want to control md5sum
wget https://genotoul-bioinfo.pages.mia.inra.fr/pangenome_hackathon/data/ztritici.tar.md5
md5sum -c ztritici.tar.md5
References¶
[1] T. Badet, U. Oggenfuss, L. Abraham, B. A. McDonald, and D. Croll, “A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici,” BMC Biol., vol. 18, no. 1, Feb. 2020, doi: 10.1186/s12915-020-0744-3.
Authors¶
- Nicolas Lapalu (nicolas.lapalu[at]inrae.fr)