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Efenaide Okoh

Candidature

PhD Candidate

Thesis Title

Using comparative genomics to review taxonomy, predict pathogenicity factors and develop typing schemes for the phytopathogenic bacterium Xanthomonas citri

Project Summary

Efenaide OkohThe species Xanthomonas citri includes pathogenic bacteria associated with disease in a diverse variety of plants and causes a wide range of economically significant diseases in agriculture and horticulture. Some of these bacteria are endemic to Australia, others are exotic. Major disease symptoms caused by these pathogens are primarily cankers, spots, blights and pustules on the plants’ aerial organs and tissues. Due to their invasiveness and outbreak potential, quarantine status has been attributed by the European Plant Protection Organisation (EPPO) to X. citri subsp. citri, X. citri subsp. aurantifolii on the A1 list and X. citri pv. fuscans on the A2 list of EPPO.
In Australia, X. citri subsp. citri is listed on the list of National Priority Plant Pests. Accurate identification of the X. citri group is a prerequisite to investigate the agricultural and biosecurity impact caused by these pathogens. Historically, identification was based upon phenotypic traits and host plant association. However, these two means of identification are unreliable and have resulted in the incorrect classification of some X. citri isolates within the subspecies and pathovar groups. DNA-based methods have been established to identify X. citri subspecies and pathovars and to evaluate whether isolates cluster in one species or whether they constitute several unrelated species.
The key aims of my PhD Thesis are to (i) rapidly identify isolates of the X. citri group through the development of the first traditional Multilocus sequence typing (MLST) scheme for this bacterial species. (ii) comparison of the pathogenicity factors of two under-studied pathovars within the citri group, pvs. anacardii and mangiferaeindicae, both effecting mango host plants. (iii) establish a new multi-level genome typing (MGT) scheme for Xanthomonas citri as a unified typing tool for population analyses and to reliably identify and differentiate pathogenic strains during incursions or outbreaks.

Publication

Okoh EB, Payne M, Lan R, Riegler M, Chapman TA, Bogema DR, (2024) 'A multilocus sequence typing scheme for rapid identification of Xanthomonas citri based on whole-genome sequencing data', Phytopathology, vol.114, no.7, pp 1480-1489

Supervisors

Professor Markus Riegler, Doctor Daniel R. Bogema, and Doctor Toni A. Chapman