Genome mining of the citrus pathogen Elsinoe fawcettii; prediction and prioritisation of candidate effectors, cell wall degrading enzymes and secondary metabolite gene clusters
Article
Article Title | Genome mining of the citrus pathogen Elsinoe fawcettii; prediction and prioritisation of candidate effectors, cell wall degrading enzymes and secondary metabolite gene clusters |
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ERA Journal ID | 39745 |
Article Category | Article |
Authors | Jeffress, Sarah (Author), Arun-Chinnappa, Kiruba (Author), Stodart, Ben (Author), Vaghefi, Niloofar (Author), Tan, Yu Pei (Author) and Ash, Gavin (Author) |
Journal Title | PLoS One |
Journal Citation | 15 (5) |
Article Number | e0227396 |
Number of Pages | 33 |
Year | 29 May 2020 |
Publisher | Public Library of Science (PLoS) |
Place of Publication | United States |
ISSN | 1932-6203 |
Digital Object Identifier (DOI) | https://doi.org/10.1371/journal.pone.0227396 |
Web Address (URL) | https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0227396 |
Abstract | Elsinoe¨ fawcettii, a necrotrophic fungal pathogen, causes citrus scab on numerous citrus varieties around the world. Known pathotypes of E. fawcettii are based on host range; additionally, cryptic pathotypes have been reported and more novel pathotypes are thought to exist. E. fawcettii produces elsinochrome, a non-host selective toxin which contributes to virulence. However, the mechanisms involved in potential pathogen-host interactions occurring prior to the production of elsinochrome are unknown, yet the host-specificity observed among pathotypes suggests a reliance upon such mechanisms. In this study we have generated a whole genome sequencing project for E. fawcettii, producing an annotated draft assembly 26.01 Mb in size, with 10,080 predicted gene models and low (0.37%) coverage of transposable elements. A small proportion of the assembly showed evidence of AT-rich regions, potentially indicating genomic regions with increased plasticity. Using a variety of computational tools, we mined the E. fawcettii genome for potential virulence genes as candidates for future investigation. A total of 1,280 secreted proteins and 276 candidate effectors were predicted and compared to those of other necrotrophic (Botrytis cinerea, Parastagonospora nodorum, Pyrenophora tritici-repentis, Sclerotinia sclerotiorum and Zymoseptoria tritici), hemibiotrophic (Leptosphaeria maculans, Magnaporthe oryzae, Rhynchosporium commune and Verticillium dahliae) and biotrophic (Ustilago maydis) plant pathogens. Genomic and proteomic features of known fungal effectors were analysed and used to guide the prioritisation of 120 candidate effectors of E. fawcettii. Additionally, 378 carbohydrate-active enzymes were predicted and analysed for likely secretion and sequence similarity with known virulence genes. Furthermore, secondary metabolite prediction indicated nine additional genes potentially involved in the elsinochrome biosynthesis gene cluster than previously described. |
Keywords | Leptosphaeria-maculans genome; phytotoxic nep1-like proteins; induced point mutation; scab diseases; elsinochrome phytotoxin; molecular analysis; avirulence gene; pathological characterization; simmondsia-chinensis; functional-analysis |
Contains Sensitive Content | Does not contain sensitive content |
ANZSRC Field of Research 2020 | 310509. Genomics |
310805. Plant pathology | |
Byline Affiliations | Centre for Crop Health |
Charles Sturt University | |
Department of Agriculture and Fisheries, Queensland | |
Institution of Origin | University of Southern Queensland |
https://research.usq.edu.au/item/q5w03/genome-mining-of-the-citrus-pathogen-elsinoe-fawcettii-prediction-and-prioritisation-of-candidate-effectors-cell-wall-degrading-enzymes-and-secondary-metabolite-gene-clusters
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2020 - Jeffress et al - journal.pone.0227396.pdf | ||
License: CC BY 4.0 | ||
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