Genome mining of the citrus pathogen Elsinoe fawcettii; prediction and prioritisation of candidate effectors, cell wall degrading enzymes and secondary metabolite gene clusters

Jeffress, Sarah and Arun-Chinnappa, Kiruba and Stodart, Ben and Vaghefi, Niloofar and Tan, Yu Pei and Ash, Gavin (2020) Genome mining of the citrus pathogen Elsinoe fawcettii; prediction and prioritisation of candidate effectors, cell wall degrading enzymes and secondary metabolite gene clusters. PloS One, 15 (5):e0227396. pp. 1-33.

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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.


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Item Type: Article (Commonwealth Reporting Category C)
Refereed: Yes
Item Status: Live Archive
Faculty/School / Institute/Centre: Current - Institute for Life Sciences and the Environment - Centre for Crop Health (24 Mar 2014 -)
Faculty/School / Institute/Centre: Current - Institute for Life Sciences and the Environment - Centre for Crop Health (24 Mar 2014 -)
Date Deposited: 22 Jul 2020 06:23
Last Modified: 27 Jul 2020 02:06
Uncontrolled 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
Fields of Research (2008): 06 Biological Sciences > 0604 Genetics > 060408 Genomics
06 Biological Sciences > 0607 Plant Biology > 060704 Plant Pathology
Identification Number or DOI: https://doi.org/10.1371/journal.pone.0227396
URI: http://eprints.usq.edu.au/id/eprint/38882

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