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 alternataa 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.

• Heaven, Thomas, Armitage, Andrew, Xu, Xiangming, Goddard, Matthew and Cockerton, Helen (2023) Dose-dependent genetic resistance to Azole fungicides found in the apple scab pathogen. Journal of Fungi, 9 (12):1136. pp. 1-18. ISSN 2309-608X (Online) (doi:https://doi.org/10.3390/jof9121136)
• Khayi, Slimane, Armitage, Andrew, Gaboun, Fatima, Meftah-kadmiri, Issam, Lahlali, Rachid, Fokar, Mohamed and Mentag, Rachid (2023) Chromosome-scale assembly uncovers genomic compartmentation of Fusarium oxysporum f. sp. albedinis, the causal agent of Bayoud disease in date palm. Frontiers in Microbiology, 14:1268051. pp. 1-14. ISSN 1664-302X (Online) (doi:https://doi.org/10.3389/fmicb.2023.1268051)
• Heaven, Thomas, Cockerton, Helen M., Xu, Xiangming, Goddard, Mat and Armitage, Andrew D. (2023) A genomic resource for the strawberry powdery mildew pathogen Podosphaera aphanis. Phytopathology, 113 (2). pp. 355-359. ISSN 0031-949X (Print), 1943-7684 (Online) (doi:https://doi.org/10.1094/PHYTO-03-22-0091-A)
• Kronmiller, Brent, Feau, Nicolas, Tabima, Javier, Ali, Shahin, Armitage, Andrew, Arrendondo, Felipe, Bailey, Bryan, Bollmann, Stephanie, Dale, Angela, Harrison, Richard, Hrywkiw, Kelly, Kasuga, Takao, McDougal, Rebecca, Nellist, Charlotte, Panda, Preeti, Tripathy, Sucheta, Williams, Nari, Ye, Wenwu, Wang, Yuanchao, Hamelin, Richard and Grunwald, Niklaus (2022) Comparative genomic analysis of 31 Phytophthora genomes reveal genome plasticity and horizontal gene transfer. Molecular Plant Microbe Interactions, 36 (1). pp. 26-46. ISSN 0894-0282 (Print), 1943-7706 (Online) (doi:https://doi.org/10.1094/MPMI-06-22-0133-R)
• Fontaine, Kévin, Fourrier-Jeandel, Céline, Armitage, Andrew, Boutigny, Anne-Laure, Crépet, Manuela, Caffier, Valérie, Gnide, Dossi Carine, Shiller, Jason, Le Cam, Bruno, Giraud, Michel, Ioos, Renaud and Aguayo, Jaime (2021) Identification and pathogenicity of Alternaria species associated with leaf blotch disease and premature defoliation in French apple orchards. PeerJ, 9:e12496. ISSN 2376-5992 (Print), 2167-8359 (Online) (doi:https://doi.org/10.7717/peerj.12496)
•  Vega-Estévez, Samuel, Armitage, Andrew, Bates, Helen J., Harrison, Richard J. and Buscaino, Alessia (2021) The genome of the CTG(Ser1) yeast Scheffersomyces stipitis is plastic. mBio, 12 (5). ISSN 2150-7511 (Print), 2150-7511 (Online) (doi:https://doi.org/10.1128/mBio.01871-21)
• Nellist, Charlotte, Armitage, Andrew, Bates, Helen, Sobczyk, Maria, Luberti, Matteo, Lewis, Laura and Harrison, Richard (2021)Comparative analysis of host-associated variation in phytophthora cactorum. Frontiers in Microbiology, 12:679936. ISSN 1664-302X (Print), 1664-302X (Online) (doi:https://doi.org/10.3389/fmicb.2021.679936)
• 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, 12:593140. ISSN 1664-302X (Online) (doi:https://doi.org/10.3389/fmicb.2021.593140)
• Adams, Thomas M., Armitage, Andrew D., Sobczyk, Maria K., Bates, Helen J., Tabima, Javier F., Kronmiller, Brent A., Tyler, Brett M., Grünwald, Niklaus J., Dunwell, Jim M., Nellist, Charlotte F. and Harrison, Richard J. (2020) Genomic investigation of the strawberry pathogen Phytophthora fragariae indicates pathogenicity is associated with transcriptional variation in three key races.Frontiers in Microbiology, 11:490. ISSN 1664-302X (Online) (doi:https://doi.org/10.3389/fmicb.2020.00490)
• Cockerton, Helen Maria, Li, Bo, Stavridou, Eleftheria, Johnson, Abigail, Karlström, Amanda, Armitage, Andrew Douglas, Martinez-Crucis, Ana, Galiano-Arjona, Lorena, Harrison, Nicola, Barber-Pérez, Nuria, Cobo-Medina, Magdalena and Harrison, Richard Jonathan (2020) Genetic and phenotypic associations between root architecture, arbuscular mycorrhizal fungi colonisation and low phosphate tolerance in strawberry (Fragaria × ananassa). BMC Plant Biology, 20:154. ISSN 1471-2229 (Online) (doi:https://doi.org/10.1186/s12870-020-02347-x)
• 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, 69 (4). pp. 669-676. ISSN 0032-0862 (Print), 1365-3059 (Online) (doi:https://doi.org/10.1111/ppa.13150)
• Armitage, Andrew, 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, 10:3124. ISSN 1664-302X (Online) (doi:https://doi.org/10.3389/fmicb.2019.03124)
• 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, 10:2905. ISSN 1664-302X (Online) (doi:https://doi.org/10.3389/fmicb.2019.02905)
• 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 Jonathan (2019) Identifying Verticillium dahliae resistance in strawberry through disease screening of multiple populations and image based phenotyping. Frontiers in Plant Science, 10:924. ISSN 1664-462X (Online) (doi:https://doi.org/10.3389/fpls.2019.00924)
• 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, 15:45. ISSN 1746-4811 (doi:https://doi.org/10.1186/s13007-019-0428-6)
• 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 (Online) (doi:https://doi.org/10.1371/journal.pone.0202305)
• 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:https://doi.org/10.1038/s41598-018-30335-7)
• 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:https://doi.org/10.1111/nph.15182)
• 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:https://doi.org/10.1371/journal.pone.0191824)
• 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:https://doi.org/10.1016/j.funbio.2015.06.012)

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 Phytophthora and Pythium, and the fungal pathogens including Fusarium, Botrytis, Colletotrichum 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 targeting management strategies based upon pathogen populations in a field.

On a fundamental level, Andrew is interested in the evolution and regulation of the regions of fungal and oomycete genomes adapted for pathogenicity. How organisms partition their genome into faster and slower evolving regions is a key interest (2- and 3-speed genomes); including study of effectors (pathogenicity genes) and identification of transposons that have played major roles in genome evolution.

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.

BSc Biology programme:

Deputy programme leader for BSc biology programme (incl. coordination of 11 modules led by NRI)

Biotechnology for Crop Improvement (BOTA 1018) - Module leader & lecturer

Evolution (OBIO 1115) - Lecturer

Microbiology and the Environment (MICR 1009) - Lecturer

MSc Global & Environmental Change / Agriculture for Sustainable Development modules:

Lecturing on Integrated Pest Management (AGRI 1039)

Lecturing on Plant Disease (BIOT 1002)

MSc Biotechnology programme

Bioinformatics (BIOT 1011) - Lecturer

Natural Product Biotechnology (BIOT 1013) – Lecturer

Current and Recent Research Projects

An enhanced toolkit for Botrytis control in protected cropping | BBSRC PACE Horticulture | PI, £1.1M | 2024 - 2028

Botrytis cinerea is a devastating pathogen of over 1000 plant species and represents the primary postharvest disease of strawberries. Beyond typical fruit rots, recent reports of severe crown-based Botrytis infections highlight an emerging challenge to the industry. An additional threat is presented by the multi-fungicide resistant species Botrytis fragariae, a novel challenge to strawberry production in the EU and USA. Monitoring and control of these three Botrytis diseases is critical, with potential losses up to 80% in the absence of control strategies.

Options for control are limited with tighter legislation on active ingredients for chemical control and due to establishment of fungicide resistance in Botrytis. As such, greater emphasis is required on the use of integrated management strategies combining in-field diagnostics for pathogen surveillance, development of durable disease resistant crops and improved deployment of microbial-biocontrols within protected systems.

Through this project we develop an advanced toolbox for precision monitoring and integrated disease management of Botrytis in protected strawberry. This work is underpinned by the fundamental study of Botrytis host-specificity, genome evolution and genomic exchange.

Understanding microbiome dynamics of crops in controlled light environments | University of Greenwich Vice Chancellor PhD Scholarship | Co-I | 2024-2027

Understanding the true Medicinal value of medicinal mushrooms | Growing Kent and Medway Business Innovation Voucher | PI | 2024-2024

Epidemiology of anthracnose on cashew genotypes and sustainable control strategies in Côte d'Ivoire | RSIF PASET visiting PhD Scholarship | PI | 2024-2024

Striga management using a host-specific fungal pathogen | University of Greenwich, REF funding | PI | 2023-2024

Phenotyping flavour: novel high-throughput assays to assess aroma and bitterness across hop breeding collections | University of Greenwich, HEIF funding | PI | 2023-2024

Distribution characterization of the fungi responsible for post-harvest rots in yams and control with biopesticides in the Cote d’Ivoire | RSIF PASET visiting PhD Scholarship | PI | 2023-2023

Development of in-field tools for early detection of fruit storage rots | BBSRC Horticultural Quality and Food Loss Network | PI | 2022-2023

Breeding better biocontrols – Identifying targets for Clonostachys rosea strain improvement through partitioning genomic regions involved in insect infection from those involved in hyphal parasitism | University of Greenwich REF funding | PI | 2022-2023

Viral diversity and coevolution with Fungal and Oomycete pathogens | University of Greenwich, Vice Chancellor PhD Scholarship | PI | 2021-2024

Developing next generation diagnostics to prevent establishment of fungal pathogens in UK fruit crops | Royal Society of Biology undergraduate studentship | PI | 2021-2021

(Current PhD/MRes students)

Medicago sativa as a model legume to understand Fusarium-legume interactions | Mahendra Paudel | MRes student, University of Greenwich | 2023 - present

Mining the untapped chemical potential of entomopathogenic fungi for sustainable agriculture and human health | Deanna Mills | LIDo DTP PhD student, University of Greenwich | 2023 - present

Safeguarding UK hop production from Verticillium nonalfalfae: Using genomics to develop race-specific diagnostics and generate Verticillium resistant hop through Host Induced Gene Silencing | Simon Thundow | SoCo DTP PhD student, University of Kent | 2022 - present

Viral diversity and coevolution with fungal and oomycete pathogens – Alexander Allman | Vice Chancellor’s PhD Scholarship, University of Greenwich | 2021 - present

(Recent completions)

A combined -omics approach to profiling the pathogenicity of Fusarium oxysporum isolates | Deanna Mills | LIDo DTP 3-month rotation project | 2023

Next generation breeding in hops | Klara Hadju | British Hop Association funded PhD studentship, NIAB EMR | 2019 - 2023

Novel ways of managing tree crop fungal diseases: Using precision diagnostic technologies to tailor disease management strategies | Thomas Heaven | Crop Science CTP PhD student | 2018 - 2024

(Visiting PhD students)

Epidemiology of anthracnose on cashew genotypes and sustainable control strategies in Côte d'Ivoire | Arsène Soro | PASET PhD visiting scholarship, Université Félix Houphouët-Boigny | 2024

Effect on climate change on the distribution characterization of the fungi responsible for post-harvest rots in yams and control with biopesticides in Côte d'Ivoire | Adjata Kamara | PASET PhD visiting scholarship, Université Félix Houphouët-Boigny | 2023

Polyphasic identification of fungal diseases and screening for resistance in African yam bean (Sphenostylis stenocarpa) germplasm to foliar and pod diseases | Olaide Ogunsanya | Commonwealth Split-site PhD Scholarship, IITA | 2022

(Undergraduate / visiting studentships)

Developing next generation diagnostics to prevent establishment of fungal pathogens in UK fruit crops | Ambrozy Boguslawski | Plant Health Undergraduate Studentship, Royal Society of Biology | 2021

Investigating Host Specificity of the Fungal Pathogen Alternaria alternata to Strawberry and Pear | Alice Smith | BMS undergraduate summer student (pg.3-5), NIAB EMR | 2019

Safeguarding UK hop production: Developing race-specific diagnostics to Verticillium albo-atrum in UK hop isolates | Giuliano Manetti | BSPP incoming Fellowship, NIAB EMR | 2019

• Deputy Programme Leader (BSc Biology)
• HPC steering group

• Microbiology Society: Eukaryotic Division (Committee member) | 2022 - present
• Microbiology Society Conference 2024 Finding the needle in the haystack, microbial surveillance in complex samples (Session organiser) | 2024
• Microbiology Society Conference 2023 Plant Microbe Interactions (Session organiser) | 2023
• BSPP workshop Practical Course on Plant Pathogen Diagnostics: From Symptoms to Sequence (Organising committee) | 2018
• Fourth International Horticulture Research Conference (Organising Committee) | 2017
• Membership of professional bodies: British Society for Plant Pathology (BSPP), British Mycological Society (BMS), American Phytopathological Society (APS), Microbiology Society.