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

被引:14
作者
Chen, Hongxin [1 ,2 ]
King, Robert [1 ]
Smith, Dan [1 ]
Bayon, Carlos [1 ]
Ashfield, Tom [1 ,3 ]
Torriani, Stefano [4 ]
Kanyuka, Kostya [1 ,5 ]
Hammond-Kosack, Kim [1 ]
Bieri, Stephane [4 ]
Rudd, Jason [1 ]
机构
[1] Rothamsted Res, Dept Protecting Crops & Environm, Harpenden, Herts, England
[2] Sun Yat sen Univ, Sch Agr, Shenzhen Campus, Shenzhen, Guangdong, Peoples R China
[3] Rothamsted Res, Crop Hlth & Protect CHaP, Harpenden, Herts, England
[4] Syngenta Crop Protect AG, Schaffhauserstr 101, CH-4332 Stein, Switzerland
[5] Natl Inst Agr Bot NIAB, 93 Lawrence Weaver Rd, Cambridge, England
基金
英国生物技术与生命科学研究理事会;
关键词
Foxtail mosaic virus; Septoria tritici; Necrotrophic effector; Essential genes; Accessory chromosomes; Dothideomycetes; Chromosome instability; Mycosphaerella spp; MYCOSPHAERELLA GRAMINICOLA PATHOSYSTEM; ZYMOSEPTORIA-TRITICI; SEXUAL REPRODUCTION; GENETIC-VARIATION; GENOME ANALYSIS; PAN-GENOME; PROTEIN; RESISTANCE; RECOMBINATION; TRANSITIONS;
D O I
10.1186/s12915-023-01520-6
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
BackgroundStudying 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.ResultsWe 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.ConclusionsThese data support the combined use of pangenomics and transcriptomics for defining genes which represent core, and potentially exploitable, weaknesses in rapidly evolving pathogens.
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页数:22
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