Knowledge for a sustainable world

BSc, MRes, PhD

Dr Andrew Armitage joined NRI as a Senior Fellow in 2020. His work centres on the basis of pathogenicity in plant disease, the diversity of pathogens in the environment and breeding crops with durable resistance. Andrew is a member of NRI’s Agriculture, Health and Environment Department, working across the Molecular Virology and Entomology, Plant Health and Postharvest Science research themes.

Before moving to NRI, Andrew was a project leader within the Genetics, Genomics and Breeding department at NIAB EMR. Based there for six years, Andrew performed research on pathosystems covering soft-fruit, top-fruit, vegetables and ornamentals alongside supporting work on mycoprotein production. He developed pipelines for a range of genomic analyses and provided support and training within the institute and for external collaborators.

Andrew holds a BSc in Ecology (Cardiff University), a MRes in Biology (Cardiff University) and a PhD investigating taxonomy, pathology and control of Alternaria alternata a non-native fungal quarantine pathogen of apple and pear (University of Warwick in partnership with FERA).

Andrew’s expertise includes genome assembly, annotation, comparative genomics, RNAseq, variant calling, amplicon sequencing, rAmpSeq and analysis of CrisprCas9 variants. He also performs bespoke analyses for organisms of interest such as pathogen effector identification, characterisation of host-adapted regions, systematics, resistance gene discovery and development of diagnostic assays.

Andrew is a bioinformatician specialising in the evolution of pathogenicity in plant disease and breeding crops for resistance to these diseases. His core research interests focus on fungi and the oomycetes, but also include bacterial and viral systems. Andrew works across a number of horticultural pathosystems, with particular interest in the oomycete pathogens of Phytophora and Pythium, and the fungal pathogens including Fusarium and Alternaria.

Research spans both fundamental science and applied science asking questions on evolution and host adaptation of a pathogen but also searching for new sources of crop resistance, developing diagnostic test for disease and targeted management based on pathogen populations in a field.

On a fundamental level, Andrew is interested in the evolution and regulation of regions in the fungal and oomycete genomes adapted for pathogenicity. Partitioning of genes into faster and slower evolving regions is a key interest (2- and 3-speed genomes); including the identification of effectors (pathogenicity genes) and transposons that shaped these regions.

On an applied level, Andrew performs genome sequencing and comparative genomics to identify loci for diagnostic tests. Targeting diagnostics to the regions of the genome that determine pathogenicity is an important step to ensure specificity to the target organism. Similar analyses are also important in identifying the basis of pesticide resistance and monitoring levels of resistance in the field. He is also engaged in pre-breeding research to identify new sources of resistance to crop disease.

  • ‘Viral diversity and coevolution with fungal and oomycete pathogens’ – Vice Chancellor’s PhD Scholarship, University of Greenwich (2021 - present)
  • ‘Developing next generation diagnostics to prevent establishment of fungal pathogens in UK fruit crops’ – Plant Health Undergraduate Studentship, Royal Society of Biology (2021)
  • ‘Novel ways of managing tree crop fungal diseases: Using precision diagnostic technologies to tailor disease management strategies’ – CTP PhD studentship, NIAB EMR (Klara Hajdu, 2018 - present)
  • ‘Next generation breeding in hops’ – British Hop Association funded PhD studentship, NIAB EMR (Thomas Heaven, 2018 - present)
  • ‘Safeguarding UK hop production: Developing race-specific diagnostics to Verticillium albo-atrum in UK hop isolates’ – BSPP incoming fellowship, NIAB EMR (Giuliano Manetti, 2019)
  • ‘Investigating Host Specificity of the Fungal Pathogen Alternaria alternata to Strawberry and Pear’ – BMS summer studentship, NIAB EMR (Alice Smith, 2019)
  • Jenkins, Sascha, Taylor, Andrew, Jackson, Alison C., Armitage, Andrew D., Bates, Helen J., Mead, Andrew, Harrison, Richard J.and Clarkson, John P. (2021) Identification and Expression of Secreted In Xylem Pathogenicity Genes in Fusarium oxysporum f. sp. pisi. Frontiers in Microbiology, 12. ISSN 1664-302X (doi:
  • Armitage, Andrew D., Cockerton, Helen M., Sreenivasaprasad, Surapareddy, Woodhall, James, Lane, Charles R., Harrison, Richard J. and Clarkson, John P. (2020) Genomics evolutionary history and diagnostics of the Alternaria alternata species group including apple and asian pear pathotypes. Frontiers in Microbiology, 10. ISSN 1664-302X (doi:
  • Armitage, Andrew D., Nellist, Charlotte, Bates, Helen, Zhang, Liqing, Zou, Xiaohua, Qing-Hua, Gao and Harrison, Richard (2021) Draft Genome Sequence of the Strawberry Anthracnose Pathogen Colletotrichum fructicola. Microbiology Resource Announcements, 9 (12):e01598-19. ISSN 2576-098X (Online) (doi:
  • Passey, Thomas A. J. , Armitage, Andrew D., Sobczyk, Maria K., Shaw, Michael W.  and Xu, Xiangming  (2020) Genomic sequencing indicates non‐random mating of Venturia inaequalis in a mixed cultivar orchard. Plant Pathology. ISSN 0032-0862 (doi:
  • Taylor, Andrew, Armitage, Andrew D., Handy, Claire, Jackson, Alison C., Hulin, Michelle T., Harrison, Richard J. and Clarkson, John P. (2019) Basal rot of Narcissus: Understanding pathogenicity in Fusarium oxysporum f. sp. narcissi. Frontiers in Microbiology, 10. ISSN 1664-302X (doi:
  • Cockerton, Helen M., Li, Bo, Vickerstaff, Robert J., Eyre, Catherine A., Sargent, Daniel J., Armitage, Andrew D., Marina-Montes, Cesar, Garcia-Cruz, Ana, Passey, Andrew J., Simpson, David W. and Harrison, Richard J. (2019) Identifying Verticillium dahliae resistance in strawberry through disease screening of multiple populations and image based phenotyping. Frontiers in Plant Science, 10. ISSN 1664-462X (doi:
  • Wilson, Fiona M., Harrison, Kate, Armitage, Andrew D., Simkin, Andrew J. and Harrison, Richard J. (2019) CRISPR/Cas9-mediated mutagenesis of phytoene desaturase in diploid and octoploid strawberry. Plant Methods, 15 (1). ISSN 1746-4811 (doi:
  • Armitage, Andrew D., Taylor, Andrew, Hulin, Michelle T., Jackson, Alison C., Harrison, Richard J., Clarkson, John P. and Rokas, Antonis (2019) Draft genome sequence of an onion basal rot isolate of Fusarium proliferatum. Microbiology Resource Announcements, 8 (1). ISSN 2576-098X (doi:
  • Armitage, Andrew D., Taylor, Andrew, Sobczyk, Maria K., Baxter, Laura, Greenfield, Bethany P. J., Bates, Helen J., Wilson, Fiona, Jackson, Alison C., Ott, Sascha, Harrison, Richard J.  and Clarkson, John P. (2018) Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae. Scientific Reports, 8:13530. ISSN 2045-2322 (Online) (doi:
  • Passey, Thomas A. J., Armitage, Andrew D., Xu, Xiangming and Rokas, Antonis (2018) Annotated draft genome sequence of the apple scab pathogen Venturia inaequalis. Microbiology Resource Announcements, 7 (12). ISSN 2576-098X (doi:
  • Hulin, Michelle T., Armitage, Andrew D., Vicente, Joana G., Holub, Eric B., Baxter, Laura, Bates, Helen J., Mansfield, John W., Jackson, Robert W. and Harrison, Richard J.  (2018) Comparative genomics of Pseudomonas syringae reveals convergent gene gain and loss associated with specialization onto cherry (Prunus avium). New Phytologist, 219 (2). pp. 672-696. ISSN 0028-646X (Print), 1469-8137 (Online) (doi:
  • Armitage, Andrew D., Lysøe, Erik, Nellist, Charlotte F. , Lewis, Laura A., Cano, Liliana M., Harrison, Richard J.  and Brurberg, May B. (2018) Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum. PLOS ONE, 13 (10). e0202305. ISSN 1932-6203 (doi:
  • Fan, Rong, Cockerton, Helen M., Armitage, Andrew D., Bates, Helen, Cascant-Lopez, Emma, Antanaviciute, Laima, Xu, Xiangming, Hu, Xiaoping and Harrison, Richard J.  (2018) Vegetative compatibility groups partition variation in the virulence of Verticillium dahliae on strawberry. PLOS ONE, 13 (2):e0191824. ISSN 1932-6203 (Online) (doi:
  • Gómez-Cortecero, Antonio, Harrison, Richard J. and Armitage, Andrew D.  (2015) Draft genome sequence of a European isolate of the apple canker pathogen Neonectria ditissima. Genome Announcements, 3 (6):e01243-15. ISSN 2169-8287 (Online) (doi:
  • Armitage, Andrew D. , Barbara, Dez J., Harrison, Richard J., Lane, Charles R., Sreenivasaprasad, Surapareddy, Woodhall, James W. and Clarkson, John P. (2015) Discrete lineages within Alternaria alternata species group: identification using new highly variable loci and support from morphological characters. Fungal Biology, 119 (11). pp. 994-1006. ISSN 1878-6146 (doi:
  • Member of the Oomycete Molecular Genomics Network
  • Organizing committee of the BSPP Practical Course in Plant pathogen Diagnostics (2018) and the Fourth International Horticulture Research Conference (2017).
  • Member of British Society of Plant Pathology, International Society for Plant Microbe Interactions, British Mycological Society, Microbiological Society, American Society for Microbiology
  • Referee for Molecular Plant Pathology, Plant Pathology, Phytopathology, Mycotaxon, European Journal of Plant Pathology, The Journal of Horticultural Science and Biotechnology.
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