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

A - Papers appearing in refereed journals

Chen, H., King, R., Smith, D., Bayon, C., Ashfield, T., Torriani, S., Kanyuka, K., Hammond-Kosack, K. E., Bieri, S. and Rudd, J. J. 2023. Combined pangenomics and transcriptomics reveals core and redundant virulence processes in a rapidly evolving fungal plant pathogen. BMC Biology. 21, p. 24. https://doi.org/10.1186/s12915-023-01520-6

AuthorsChen, H., King, R., Smith, D., Bayon, C., Ashfield, T., Torriani, S., Kanyuka, K., Hammond-Kosack, K. E., Bieri, S. and Rudd, J. J.
Abstract

Background
Studying genomic variation in rapidly evolving pathogens potentially enables identification of genes supporting their “core biology”, being 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.

KeywordsFoxtail Mosaic Virus; Septoria tritici; Necrotrophic effector; Essential genes; Accessory chromosomes; Dothideomycetes; Chromosome instability; Mycosphaerella spp
Year of Publication2023
JournalBMC Biology
Journal citation21, p. 24
Digital Object Identifier (DOI)https://doi.org/10.1186/s12915-023-01520-6
Open accessPublished as ‘gold’ (paid) open access
FunderBiotechnology and Biological Sciences Research Council
Funder project or codeDFW - Designing Future Wheat - Work package 2 (WP2) - Added value and resilience
20:20 Wheat [ISPG]
Delivering Sustainable Wheat (WP2): Delivering Resilience to Biotic Stress
Growing Health (WP1) - bio-inspired solutions for healthier agroecosystems: Understanding biointeractions
Resilient Farming Futures (WP1): Understanding impacts of single and compound climate policy and biotic stresses on agroecosystem ‘resilience’
Publisher's version
Supplemental file
Output statusPublished
Publication dates
Online06 Feb 2023
Publication process dates
Accepted19 Jan 2023
PublisherBiomed Central Ltd
ISSN1741-7007

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