A global pangenome for the wheat fungal pathogen Pyrenophora tritici-repentis and prediction of effector protein structural homology

• Published in: Microbial genomics 2022-10, Vol.8 (10)
• Main Authors: Moolhuijzen, Paula M, See, Pao Theen, Shi, Gongjun, Powell, Harold R, Cockram, James, Jørgensen, Lise N, Benslimane, Hamida, Strelkov, Stephen E, Turner, Judith, Liu, Zhaohui, Moffat, Caroline S
• Format: Article
• Language: English
• Subjects: Ascomycota; Host-Pathogen Interactions - genetics; Mycotoxins - genetics; Mycotoxins - metabolism; Plant Diseases - microbiology; Structural Homology, Protein; Triticum - genetics; Triticum - metabolism; Triticum - microbiology
• ISSN: 2057-5858; 2057-5858
• DOI: 10.1099/mgen.0.000872

The adaptive potential of plant fungal pathogens is largely governed by the gene content of a species, consisting of core and accessory genes across the pathogen isolate repertoire. To approximate the complete gene repertoire of a globally significant crop fungal pathogen, a pan genomic analysis was undertaken for (Ptr), the causal agent of tan (or yellow) spot disease in wheat. In this study, 15 new Ptr genomes were sequenced, assembled and annotated, including isolates from three races not previously sequenced. Together with 11 previously published Ptr genomes, a pangenome for 26 Ptr isolates from Australia, Europe, North Africa and America, representing nearly all known races, revealed a conserved core-gene content of 57 % and presents a new Ptr resource for searching natural homologues (orthologues not acquired by horizontal transfer from another species) using remote protein structural homology. Here, we identify for the first time a non-synonymous mutation in the Ptr necrotrophic effector gene , multiple copies of the inactive within an isolate, a distant natural homologue of a known necrotrophic effector (SnTox3), and clear genomic break points for the effector horizontal transfer region. This comprehensive genomic analysis of Ptr races includes nine isolates sequenced via long read technologies. Accordingly, these resources provide a more complete representation of the species, and serve as a resource to monitor variations potentially involved in pathogenicity.