Poster Presentation Australian Society for Microbiology Annual Scientific Meeting 2022

Unbiased analysis of Australian and International Xanthomonas campestris isolate genomes reveals novel host specificity and potential pathogenesis associated genes. (#111)

Daniel Bogema 1 , John Webster 1 , Efenaide Okoh 2 , Linda Falconer 1 , Leena Koop 1 , Rachael Mann 3 , Michael Liu 4 , Aaron Darling 4 , Len Tesoriero 1 , Toni Chapman 1
  1. Biosecurity & Food Safety, NSW Department of Primary Industries, Menangle, New South Wales, Australia
  2. Hawkesbury Institute of the Environment, Western Sydney University, Penrith, NSW, Australia
  3. Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio, Bundoora, Victoria, Australia
  4. The ithree institute, University of Technology Sydney, Ultimo, NSW, Australia

Xanthomonas campestris is a host-specific bacterial pathogen of plants currently identified to consist of at least three pathovars. Pathovar (pv.) campestris (Xcc) causes black rot of cruciferous plants, pv. incanae (Xci) is linked to bacterial blight of ornamental cruciferous plants, and pv. raphani (Xcr) causes leaf spot disease of Crucifereae and Solanaceae. While all pathovars are spread internationally, Xcc causing Black rot is devastating to commercial Brassica crops, including cabbage, cauliflower, broccoli, kale, and brussels sprouts. The taxonomy of the Xanthomonas genus has been historically problematic and recent molecular investigations have caused substantial changes.

We sequenced and examined the genomes of 264 X. campestris isolates sourced from recent pathological investigations, previous studies of X. campestris pathology and diagnosis, the NSW Plant Pathology & Mycology Herbarium and other international culture collections. This included a substantial number of non-pathogenic, Xci and Xcr isolates. Further, using an unbiased ANI-based species classification method we identified numerous X. campestris isolates in a larger sequence collection that had been misclassified using historical methods. Including Xcc found on unusual hosts.

In Australia we identified a strain structure that was largely consistent with international isolates. Further analysis of a cohort collected from SE QLD in a single year showed high diversity, particularly within the same farm. Importantly, the inclusion of multiple non-pathogenic revealed novel genes highly associated with black rot causing Xcc.

While this collection primarily consists of Xcc affecting Brassica growing regions of south-eastern Australia, we have also generated the first sequences of several important historical isolates including the pathotype strain of Xcr. In total this isolate collection triples the available public dataset of X. campestris assembled genome sequences; spans 72 years, 6 continents, and 11 host species and provides insight into the taxonomy, epidemiology and pathology of this important plant pathogen.