Login | Request Account (DAF staff only)

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

Share this record

Add to FacebookAdd to LinkedinAdd to XAdd to WechatAdd to Microsoft_teamsAdd to WhatsappAdd to Any

Export this record

View Altmetrics

Jeffress, S., Arun-Chinnappa, K., Stodart, B., Vaghefi, N., Tan, Y. P. and Ash, G. (2019) Genome mining of the citrus pathogen Elsinoë fawcettii; prediction and prioritisation of candidate effectors, cell wall degrading enzymes and secondary metabolite gene clusters. bioRxiv . 2019.12.19.882142.

[img]
Preview
PDF
1MB

Article Link: https://doi.org/10.1101/2019.12.19.882142

Publisher URL: https://www.biorxiv.org/content/biorxiv/early/2019/12/19/2019.12.19.882142.full.pdf

Abstract

Elsinoë 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. 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 203 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 77 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. A further 21 secondary metabolite clusters were predicted, some with similarity to known toxin producing gene clusters. The candidate virulence genes predicted in this study provide a comprehensive resource for future experimental investigation into the pathogenesis of E. fawcettii.

Item Type:Article
Business groups:Biosecurity Queensland
Subjects:Science > Botany > Genetics
Plant culture > Fruit and fruit culture
Plant pests and diseases > Plant pathology
Live Archive:09 Jan 2020 01:58
Last Modified:03 Sep 2021 16:45

Repository Staff Only: item control page

Downloads

Downloads per month over past year

View more statistics