Daniel McKnight

Daniel McKnight

Bioinformatician in plant pathogen genomics and biosecurity

I use genomics and phylogenetics to work out which bacteria are threatening Australian crops. My PhD, with the University of Technology Sydney and NSW DPIRD, described four new Xanthomonas species and made the first Australian record of Xanthomonas cannabis.

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Schematic family tree of Xanthomonas species from my research A simplified tree showing four new species I described, the first Australian record of Xanthomonas cannabis, and other Xanthomonas. Not to scale. X. rydalmerensis X. bundabergensis X. medicagonis X. tesorieronis X. cannabis other Xanthomonas other Xanthomonas
New species I described First Australian record Schematic, not to scale.

Research

Xanthomonas is a genus of plant-pathogenic bacteria whose name comes from the yellow pigment in its colonies. Many Australian isolates sat in culture collections for decades without a species name. I sequenced and compared their genomes, tested whether they cause disease, and placed them on the tree.

The work sits between the lab and the computer: bacterial genome assembly, phylogenetics, pangenomics, virulence factor and genomic island identification, plus the plant assays and qPCR diagnostics that back the results up.

  • Xanthomonas rydalmerensisIsolated from strawberry at Rydalmere in 1976. Carries few virulence-associated factors and did not cause disease in a pathogenicity assay.
  • Xanthomonas bundabergensisIsolated from strawberry at Bundaberg in 2010.
  • Xanthomonas medicagonisIsolated from lucerne (Medicago sativa) at Tatham in 1981.
  • Xanthomonas tesorieronisIsolated from strawberry at Rockley in 1976. Named for plant pathologist Leonard Tesoriero.
  • Xanthomonas cannabis in AustraliaFive historical isolates from zinnia and zucchini. Two lines of evidence, genomes and plant assays, show an emerging pathogen with genomic islands linked to virulence and drug resistance.

Publications

  1. Comparative genomics of ‘Xanthomonas cannabis’ reveals an emerging, diverse pathogen

    McKnight DJE, Clackson L, Wong-Bajracharya J, Webster J, Worden P, Snijders F, Okoh EB, Djordjevic SP, Chapman TA, Bogema DR. Microbial Genomics 11(11), 2025. doi:10.1099/mgen.0.001588

    Reports the presence of this pathogen in Australia and characterises how diverse it is.

  2. Xanthomonas bundabergensis sp. nov., Xanthomonas medicagonis sp. nov. and Xanthomonas tesorieronis sp. nov.: three members of group 1 Xanthomonas

    McKnight DJE, Wong-Bajracharya J, Okoh EB, Snijders F, Lidbetter F, Webster J, Haughton M, Djordjevic SP, Bogema DR, Chapman TA. International Journal of Systematic and Evolutionary Microbiology 75, 006686, 2025. doi:10.1099/ijsem.0.006686

    Describes three new species from four historical Australian isolates.

  3. Xanthomonas rydalmerensis sp. nov., a non-pathogenic member of Group 1 Xanthomonas

    McKnight DJE, Wong-Bajracharya J, Okoh EB, Snijders F, Lidbetter F, Webster J, Haughton M, Darling AE, Djordjevic SP, Bogema DR, Chapman TA. International Journal of Systematic and Evolutionary Microbiology 74(3), 006294, 2024. doi:10.1099/ijsem.0.006294

    Describes a new species from strawberry and shows it is non-pathogenic.

  4. Paper in Plant Pathology (add title)

    McKnight DJE et al. Plant Pathology (British Society for Plant Pathology). doi:10.1111/ppa.14130

Full list and citation counts on Google Scholar and ORCID.

Experience and education

Employment

2021 to present
Technical assistantBiotechnology and Plants laboratories, NSW Department of Primary Industries and Regional Development (DPIRD). High-throughput, NATA-accredited laboratory work.
2020 to 2021
Electrical contractorDevika
2020
Summer casual researcherYu Research Group
2018
Biochemistry internVenus Shell Systems
2015 to 2020
Sales assistantJaycar Electronics, Wollongong

Education

2021 to 2025
Doctor of Philosophy (thesis submitted)Collaborative project between the University of Technology Sydney and NSW DPIRD
2020
Bachelor of Science (Honours), first classUniversity of Wollongong
2016 to 2019
Bachelor of Science (Biological Sciences)University of Wollongong

Awards and certificates

2024
Store and handle dangerous goods and hazardous substances (TLID0021)
2023
Vice-Chancellor’s Conference FundUniversity of Technology Sydney
2021
Australian Research Council (ARC) Linkage scholarship and stipend

Skills

Genomics and phylogenetics. Bacterial genome assembly, phylogenetics, genomic and pangenomic analysis, virulence factor and genomic island identification.

Programming and pipelines. Python, R and GNU Bash from five years of bioinformatics and computational biophysics research. I build automated pipelines with QC checkpoints, error handling and reproducibility.

Molecular diagnostics. Developing and validating qPCR primers, including an assay for pre-symptomatic detection of Xanthomonas campestris in broccoli.

Data analysis. Data manipulation and visualisation for published papers and my thesis.

Collaboration. Coordinated research across 12 co-authors from four institutes. I taught myself computational biophysics and bioinformatics coming from a biological science background.

Community

2023 to present
VolunteerIllawarra Potters Inc., a community pottery studio
2020
Student representativeSMAH honours course, University of Wollongong
2019
Learning Labs volunteerTaught high school students in summer STEM classes, University of Wollongong
2018 to 2019
BioNetSocial and support network for biology students, University of Wollongong

Contact

I’m looking to keep contributing to Australian biosecurity. If you work on plant disease, diagnostics or pathogen genomics, get in touch.