Genome mining and comparative genomics of Elsinoe species, causing scab diseases on citrus and jojoba in Australia, for the prediction of virulence genes

Genome mining and comparative genomics of Elsinoe species, causing scab diseases on citrus and jojoba in Australia, for the prediction of virulence genes

Elsinoë fawcettii and E. australis are necrotrophic fungal pathogens which cause citrus scab and sweet orange scab, respectively. E. fawcettii causes disease on a wide range of citrus varieties around the world, while E. australis causes disease on sweet orange in South America. Recently, novel pathotypes of E. australis have been identified in Australia, including the Jojoba Black Scab (JBS) pathotype which causes black scab disease on jojoba and the Finger Lime (FL) pathotype which causes disease on finger lime fruit. As citrus is an economically important crop in Australia, research into pathogens of citrus and closely related pathogens is needed. It is known that species of Elsinoë produce elsinochrome, a secondary metabolite which contributes towards virulence in a non-host selective manner. However, the pathogen-host processes occurring before the release of elsinochrome are not understood, yet host-specificity is well known among the species and pathotypes suggesting such processes occur. This study produced genome assemblies for two species of Elsinoë, including four E. fawcettii (25.8 – 26.4 Mb), four E. australis JBS pathotype (26.6 Mb) and one E. australis FL pathotype (23.8 Mb). Phylogenetic analyses were conducted indicating the E. fawcettii pathotypes were very closely related, while the E. australis pathotypes were distinct from one another. Genome mining for pathogenicity related genes indicated that Elsinoë have a repertoire of predicted candidates including five secondary metabolite gene clusters, in addition to elsinochrome, that are conserved among Elsinoë, as well as 186 - 219 cell wall degrading enzymes and 94 – 120 prioritised effectors which may be enabling their host-specific pathogenesis pathways. Comparative analyses with other Elsinoë and with other fungal plant pathogens (Botrytis cinerea, Parastagonospora nodorum, Pyrenophora tritici-repentis, Sclerotinia sclerotiorum, Zymoseptoria tritici, Leptosphaeria maculans, Pyricularia oryzae (syn. Magnaporthe oryzae), Rhynchosporium commune, Verticillium dahliae and Ustilago maydis) assisted with the shortlisting of candidate effectors. Genomic regions of potential plasticity were also identified, indicating predicted virulence related genes of some Elsinoë, such as candidate effectors, were more likely to be located in the close vicinity of transposable elements and adenine and thymine (AT)-rich regions. This provides an insight into the potential maintenance of pathogenicity-related genes of Elsinoë, in addition it highlights regions of the genome which may hold further virulence factors not predicted by current methods. This study has established a comprehensive resource for future experimental validation of genes which Elsinoë utilise in order to infect plants in a host selective manner.

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