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Series GSE222164 Query DataSets for GSE222164
Status Public on Jan 13, 2023
Title Combined pangenomics and transcriptomics reveals core and redundant virulence processes in a rapidly evolving fungal plant pathogen
Organisms Triticum aestivum; Zymoseptoria tritici
Experiment type Expression profiling by high throughput sequencing
Summary Background: 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. Results:We constructed a pangenome of 18 European field isolates, with 12 also subjected to RNAseq transcription profiling during infection. Combining this data, we predicted a “core” gene set comprising 9807 sequences which were; (1) present in all isolates; (2) lacking inactivating polymorphisms ; and (3) expressed by all isolates. A large accessory genome, consisting of 45% of the total genes was also defined. We classified genetic and genomic polymorphism at both chromosomal and individual gene scales. Proteins required for essential functions including virulence, had lower-than average sequence variability amongst core genes. Both core and accessory genomes encoded many small, secreted candidate effector proteins that likely interact with plant immunity. Viral vector-mediated transient in planta overexpression of 88 candidates failed to identify any which induced leaf necrosis characteristic of disease. However, functional complementation of a non-pathogenic deletion mutant lacking five core genes, demonstrated that full virulence was restored by re-introduction of the single gene exhibiting least sequence polymorphism and highest expression. Conclusions:These data support the combined use of pangenomics and transcriptomics for defining genes which represent core, and potentially exploitable, weaknesses in rapidly evolving pathogens.
Overall design Z.tritici expression in vitro and in planta (at 6 and 9 days post infection)
Contributor(s) Chen H, King R, Smith D, Bayon C, Ashfield T, Torriani S, Kanyuka K, Hammond-Kosack K, Bieri S, Rudd J
Citation(s) 36747219
Submission date Jan 04, 2023
Last update date Mar 02, 2023
Contact name Daniel Smith
Organization name Rothamsted Research
Department IDE
Street address West Common
City Harpenden
State/province Hertfordshire
ZIP/Postal code AL5 2JQ
Country United Kingdom
Platforms (2)
GPL23509 Illumina HiSeq 4000 (Triticum aestivum)
GPL33003 Illumina HiSeq 4000 (Zymoseptoria tritici)
Samples (114)
GSM6916835 In-planta mock infection, 6 days post infection, replicate 1
GSM6916836 In-planta mock infection, 6 days post infection, replicate 2
GSM6916837 In-planta mock infection, 6 days post infection, replicate 4
BioProject PRJNA918399

Download family Format
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Supplementary file Size Download File type/resource
GSE222164_Pangenome_Zt_17I_IPO323_v3.fasta.gz 12.6 Mb (ftp)(http) FASTA
GSE222164_ztriticiPangenomePlantaCounts.txt.gz 2.3 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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