Combined pangenomics and transcriptomics reveals core and redundant virulence processes in a rapidly evolving fungal plant pathogen

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Retrieved: 22:55 26 Nov 2024 (UTC)
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Abstract

Studying genomic variation in rapidly evolving pathogens potentially enables definition of genes supporting their “core biology” present, functional and expressed by all strains or “flexible biology”, varying between strains. Genes supporting flexible biology may be considered to be “accessory”, whilst the “core” gene set is likely to be important for common features of a pathogen species biology, including virulence on all host genotypes. The wheat-pathogenic fungus Zymoseptoria tritici represents one of the most rapidly evolving threats to global food security and was the focus of this study.

Methods

The primary raw data is DNA and RNA sequencing. Short-read Illumina DNA sequences were used to assemble 17 Zymoseptoria tritici genomes and the gene expression of these genomes in-vitro and in-planta at several time points was assessed by Illumina RNA sequencing.
A pangenome gene sequence and annotation was derived from a comparison of the seventeen new genomes with the reference genome IPO323. The RNAseq data was mapped to the pangenome coding sequences, and a gene expression count file was generated.
All the raw and derived data that the work is based on is archived in public repositories, accessible after publication, using the NCBI BioProject code PRJNA890236 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA890236) and the Rothamsted repository.
Derived Data: gene sequences and annotation:
-Pangenome_Zt_17I_IPO323_v3.fasta
-annotation_pangenomveV3_2.gtf
Derived Data: Gene Expression Counts
-GSE222164_Pangenome_Zt_17I_IPO323_v3.fasta.gz
-GSE222164_ztriticiPangenomePlantaCounts.txt.gz
Fungal strains isolated from field samples by Syngenta in the following countries: France, Germany, Ireland, Great Britain, Belgium, Spain, Italy, Sweden, Poland, Czech republic and Slovakia.

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Responsible Person Jason Rudd
Research Infrastructure Used Bioinformatics
Data Locations Rothamsted Research shared drives
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