• Computational biology and bioinformatics.
  • Oomycete and bacterial plant pathogens.
  • Systems biology of plant-pathogen interactions.
  • Comparative genomics of plant pathogens.

Research interests

My research centres on plant-pathogen interactions: I aim to understand what it is about microbial plant pathogens that enables them to infect plants, and what it is is about plants that allows microbes to cause disease on them. As a computational biologist, my work involves computational and mathematical analysis of biological data, such as sequence data, transcription profiles, and networks of metabolic and regulatory processes.

Systems biology

  • Plant cells contain complex systems of signalling, regulatory and metabolic networks (Pritchard and Birch, 2011) that are perturbed by invading microbes which introduce effector proteins and other molecular species into the host. Invaded plants detect molecular components of the invading pathogen and changes to their cellular networks, often responding with effective resistance. I am interested in the implications of the dynamics and structure of cellular networks for the development of plant disease caused by microbial pathogens.

Genomics and comparative genomics of plant pathogens

Oomycete and bacterial plant pathogens

  • Much of my work is in support of the practical goal of reducing the impact of severe and financially significant crop diseases caused by oomycete and bacterial plant pathogens, such as Phytophthora infestans and Dickeya species. In order to understand the relationship between our models and the outcome of infection, we need to appreciate both the biological and the mathematical details of the problem. Oomycete effector proteins (Birch et al. 2009, Birch et al. 2006, Armstrong et al. 2005), and interactions with plant defences (Gilroy et al. 2007). Microarray design and analysis of gene expression profiles in bacterial plant pathogens (McNally et al. 2012Antunez-Lamas et al. 2009, Ravirala et al. 2007). Persistence of human pathogenic bacteria on plants (Holden et al. 2008).

Computational Biology and Bioinformatics

  • Bioinformatics and mathematics are the tools that I use to study and make sense of biological sequences and other data. I am interested in visualisation tools for large datasets, and a collaboration in this area with Ian Toth, Michel Perombelon, and Prof. Elaine Shemilt of the Duncan of Jordanstone College of Art and Design resulted in exhibitions in Dundee and Singapore. I have also contributed code to open source bioinformatics projects, including Biopython. Visualisation of comparative genomic data (Pritchard et al. 2006). Galaxy (Cock et al. 2013). Tablet (Milne et al. 2013). Directed evolution and error-prone PCR (Pritchard et al. 2005). Protein sequence-structure-function analysis, including covariation analysis (Pritchard et al. 2003, Pritchard et al. 2001, Pritchard and Dufton 2000, Pritchard and Dufton, 1999)

Collaborations 

  • Plant pathogen research  is a multidisciplinary effort, and I collaborate with a number of researchers in a range of fields, in the UK and internationally.

Journals

Books / chapters

Technical / contract reports

  • Avrova, A.O.; Birch, P.R.J.; Hein, I.; Jones, J.T.; Pritchard, L. (2010) Functional analysis of pathogen effectors: how to go from genomics to durable resistance., Annual Report of the Scottish Crop Research Institute for 2009, 39-41.
  • Whisson, S.C.; Boevink, P.; Pritchard, L.; Avrova, A.O.; Morales, J.; Birch, P.R.J. (2006) Effector protein translocation in the Phytophthora infestans – potato infection., Annual Report of the Scottish Crop Research Institute for 2006, pp24-25.
  • Toth, I.K.; Pritchard, L.; Holeva, M.C.; Hyman, L.J.; Bell, K.S.; Whisson, S.C.; Avrova, A.O.; Birch, P.R.J. (2004) New discoveries with Erwinia genomics., Annual Report of the Scottish Crop Research Institute for 2002/2003, p101.

Conference papers

  • Green, S.; Cooke, D.E.L.; Frederickson-Matika, D.; Clark, B.; Randall, E.; Clark, M.; Pettit, T.; Dunn, M.; Schlenzig, A.; Pritchard, L.; Thorpe, P.; Cock, P.; Barbrook, J. (2019) Phytophthora communities in UK plant nurseries and links to management practice: opportunities for mitigation through accreditation., Presentation at the 9th Meeting of the IUFRO Working Party 7.02.09: Phytophthora in Forests and Natural Ecosystems, Sardinia 17-25 October 2019.
  • Cooke, D.E.L.; Randall, E.; Clark, B.; Thorpe, P.; Cock, P.J.; Pritchard, L.; Pettitt, T.; Frederickson-Matika, D.; Green, K.R. (2019) Phytophthora eDNA barcoding for natural ecosystem surveillance., 20th Oomycete Molecular Genetics Network Annual Meeting, Scottish Association for Marine Science (SAMS), Oban, 10-12 July 2019. Presentation.
  • Cooke, D.E.L.; Randall, E.; Clark, B.; Thorpe, P.; Pritchard, L.; Pettitt, T.; Frederickson-Matika, D.; Green, S. (2018) The validation of eDNA barcoding in the study of Phytophthora diversity for plant health testing and natural ecosystem surveillance., Presentation at The 6th International Oomycetes Workshop: Phytophthora, Pythium, Downy Mildews and Related Genera 2018, Boston, USA. 28 July 2018.
  • Cooke, D.E.L.; Pritchard, L.; Thorpe, P.; Green, S.; Taylor, A. (2017) eDNA and plant pathogen metabarcoding., Presentation at SNH Sharing Good Practice, The Use of Technology to Gather Data about the Natural Environment, Battleby, Perth, UK, 7 June 2017.
  • Cooke, D.E.L.; Prigigallo, M.I.; Schena, L.; Randall, E.; Squires, J.N.; Clark, B.; Thorpe, P.; Pritchard, L.; Studholme, D.J.; Boonham, N.; Henricot, B.; Green, S. (2017) Testing in situ water sampling and metabarcoding protocols to detect Phytophthora diversity for plant health testing and natural ecosystem surveillance., Presentation at the Eighth meeting of the International Union of Forest Research Organizations (IUFRO) Working Party S07.02.09. SaPa, Vietnam, 19-25 March 2017.
  • Toth, I.K.; Saddler, G.; Cahill, G.; Elphinstone, J.; Wale, S.; Gibson-Poole, S.; Humphris, S.; Pritchard, L.; Campbell, E.; Watts, L. (2017) Developing an IPM toolbox for blackleg disease., European Association for Potato Research triennial conference, Versailles, Paris, France. 9-14 July 2017.
  • Toth, I.K.; Humphris, S.; Pritchard, L.; Skelsey, P. (2014) Environmental spread of Pectobacterium and Dickeya: diagnostics to modelling., Euphresco Pectobacterium and Dickeya Workshop, Bern, Switzerland, 25 November 2014.
  • Cooke, D.E.L.; Squires, J.N.; Randall, E.; Pritchard, L.; Birch, P.R.J. (2013) Tracking effector diversity in populations of Phytophthora infestans., COST-FA1208 Meeting on Pathogen-informed Strategies for Sustainable Broad-spectrum Crop Resistance, Birnam, 9-11 October 2013.
  • Toth, I.K.; Pritchard, L.; Humphris, S.; Douglas, E.; Birch, P.R.J. (2013) Genomic approaches to research on Pectobacterium and Dickeya species., International Congress of Plant Pathology (ICPP), Beijing, China, 25 – 30 August 2013.
  • Pritchard, L.; Humphris, S.; Campbell, E.; Elphinstone, J.; Saddler, G. (2013) The environment and pathogen detection: how genomics research on the bacterial plant pathogens Pectobacterium and Dickeya makes a difference to potato growers., 97th Annual Meeting of the Potato Association of America, Quebec City, Canada, 28 July – 1 August 2013.
  • Toth, I.K.; Pritchard, L.; Humphris, S.; Campbell E.; Birch, P.R.J. (2013) Pathogenicity and resistance: how genomics research on the bacterial plant pathogens Pectobacterium and Dickeya makes a difference to potato growers., 97th Annual Meeting of the Potato Association of America, Quebec City, Canada, 28 July – 1 August 2013.
  • Pritchard, L.; Toth, I.K. (2012) Dickeya genomics at JHI – latest progress., Euphresco ERA-NET on Dickeya, 5-6 November 2012.
  • Toth, I.K.; Pritchard, L.; Humphris, S. (2012) Designing ‘D. solani’ diagnostics the genome way., Euphresco ERA-NET on Dickeya, 5-6 November 2012.
  • Toth, I.K.; Holden, N.; Pritchard, L. (2012) Genomics research on Pectobacterium and Dickeya species: disease, ecology and diagnosis., Molecular Plant Microbe Interactions (MPMI) Conference, Kyoto, Japan, 27 July 2012.
  • Toth, I.K.; Holden, N.; Pritchard, L. (2012) We only find what we look for: can enteric pathogens of animals live on and be spread by plants?, KNVM/NVMM Dutch Microbiology Society, Papendal, the Netherlands, 17 April 2012.
  • Humphris, S.; Campbell, E.; Pritchard, L.; Elphinstone, J.; Parkinson, N.; Saddler, G.; Toth, I.K. (2011) Dickeya solani in the environment., Euphresco Meeting on Dickeya, 7 November 2011.
  • Pritchard, L.; Toth, I.K. (2011) How to sequence a bacterial genome., Euphresco Meeting on Dickeya, 7 November 2011.
  • Toth, I.K.; Pritchard, L. (2011) Genomics leads to new discoveries and practical solutions to blackleg disease control., European Association for Potato Research (EAPR) Conference, Oulu, Finland, 24-29 July 2011.
  • Toth, I.K.; Pritchard, L. (2011) Whole genome microarrays: quorum sensing and species-specific genomic islands in Pectobacterium atrosepticum., Southern African Society for Plant Pathology, Kruger National Park, South Africa, 23-26 January 2011.
  • Whisson, S.C.; Gilroy, E.M.; Avrova, A.O.; Tian, Z.D.; Breen, S.; Armstrong MR.; Squires, J.; Vieeshouwers, V.; McLellan, H.; Seman, Z.; Kandel, K.; Boevink, P.C.; Pritchard, L.; Hein, I.; Cooke, D.E.L.; Birch, P.R.J.; (2011) Phytophthora infestans effectors in late blight disease development and exploitation for disease control., 18th Triennial Conference of the European Association for Potato Research, Oulu, Finland, 24-29 July 2011.
  • Toth, I.K.; Liu, H.; Coulthurst, S.J.; Humphris, S.; Douglas, E.; Hedley, P.E.; Booth, C.; Ravensdale, M.; Burr, T.; Takle, G.; Bruberg, M.; Birch, P.R.J.; Salmond, G.P.C.; Francois, P.; Schrenzel, J.; Pritchard, L. (2010) Whole genome microarrays to investigate the potato pathogen Pectobacterium atrosepticum species-specific genomic islands and quorum sensing., International Conference on Plant Pathogenic Bacteria (ICPPB). Reunion, 7-11 June 2010.
  • Toth, I.K.; Humphris, S.; Douglas, E.; Pritchard, L.; Birch, P.R.J.; Takle, G.; Brurberg, M.B.; (2010) Genomics uncovers a life on plants away from disease for the potato pathogen Pectobacterium atrosepticum., International Erwinia Workshop, Reunion, 5-6 June 2010.
  • Toth, I.K.; Birch, P.R.J.; Pritchard, L.; Liu, H.; Hedley, P.E.; Humphris, S.; Douglas, E.; Gilroy, E.M.; Moleleki, L.N.; Ravensdale, M.; Hardy, D.; Mayer, C.; Husmeier, D.; Lin, K. (2010) From bully to master tactician: a genomics approach reveals unexpected traits in the life of the bacterial plant pathogen Pectobacterium., IFR Seminar Series. Institute of Food Research, 4 March 2010.
  • Toth, I.K.; Birch, P.R.J.; Pritchard, L.; Humphris, S.N.; Douglas, E.; Gilroy, E.M.; Morris, J.; Hedley, P.E. (2010) Using genomics approaches to investigate the life of the bacterial potato pathogen Pectobacterium atrosepticum., COST 872 Nemagenics. Exploiting genomics to understand plant-nematode interactions, 4th Annual Meeting. Lisbon, Portugal, 24-27 May 2010.
  • McLellan, H.; Tian, Z.D.; Avrova, A.O.; Gilroy, E.M.; Pritchard, L.; Whisson, S.C.; Birch, P.R.J. (2010) Identification of RXLR effectors essential for virulence in Phytophthora infestans., Oomycete Molecular Genetics Network Congress, Toulouse, France, 6-8 June 2010.
  • Breen, S.; Gilroy, E.M.; Armstrong, M.R.; Morales, J.G.; Hein, I.; Douglas, E.; Boevink, P.; McLellan, H.; Randall, E.; Tian, Z.D.; Avrova, A.O.; Pritchard, L.; Lokossou, A.A.; Govers, F.; van der Vossen, E.A.G.; Vleeshouwers, V.G.A.A.; Brunner, F.; Whisson, S.C.; Birch, P.R.J. (2010) Avr2, an RXLR effector from Phytophthora infestans., Oomycete Molecular Genetics Network Congress, Toulouse, France, 6-8 June 2010.
  • Armstrong, M.R.; Boevink, P.; Bukharova, T.; McLellan, H.; Ramos, M.; Gilroy, E.M.; Pritchard, L.; Whisson, S.C.; Beynon, J.; Birch, P.R.J. (2010) Identifying candidate host ‘targets’ of Phytophthora infestans translocated RXLR proteins., Oomycete Molecular Genetics Network Congress, Toulouse, France, 6-8 June 2010.
  • Gilroy, E.M.; Hein, I.; McLellan, H.; Breen, S.; Engelhardt, S.; Tian, Z.D.; Seman, Z.A.; Pritchard, L.; Armstrong, M.R.; Randall, E.; Avrova, A.O.; Cooke, D.E.L.; Lees, A.K.; Vleeshouwers, V.G.A.A.; van West, P.; Whisson, S.C.; Birch, P.R.J. (2010) Using knowledge of RXLR effectors to seek durable resistance., Oomycete Molecular Genetics Network Congress, Toulouse, France, 6-8 June 2010.
  • Toth, I.K.; Pritchard, L.; Birch, P.R.J.; Humphris, S.N.; Douglas, E.; Liu, H.; Morris, J.A.; Hedley, P.E. (2009) The humble bacterium: what would Darwin have made of this master of evolution?., BSPP Presidential Meeting: Darwin to Disease: Crops and Their Pathogens, Oxford, 22 September 2009.
  • Gilroy, E.M.; Armstrong, M.R.; Bos, J.; Taylor, R.; Morales, J.; Hein, I.; Douglas, E.; Boevink, P.; Avrova, A.O.; Breen, S.; van West, P.; Pritchard, L.; Whisson, S.C.; Sadanandom, A.; Kamoun, S.; Birch, P.R.J. (2009) Functional analysis of Phytophthora infestans RXLR effectors Avr2 and Avr3a., Fungal Genetics Conference, Asilomar Conference Grounds, Pacific Grove, California, USA, 17-22 March 2009.

Conference posters / abstracts

  • Pritchard, P.; Cock, P.J.A.; Thorpe, P.; Randall, E.; Green, S.; Cooke, D.E.L. (2019) Metabarcoding diagnostics of Phytophthora species in environmental samples., XVIII International Congress on Molecular Plant-Microbe Interactions, Glasgow, UK, 14-18 July 2019. Abstract.
  • Green, S.; Cooke, D.E.L.; Frederickson-Matika, D.; Clark, B.; Randall, E.; Thorpe, P.; Pritchard, L.; Cock, P.; Pettitt, T.; Schlenzig, A.; Barbrook, J. (2019) PHYTO-THREATS: An analysis of Phytophthora communities in plant nurseries., Proceedings of XXV IUFRO World Congress 2019: Forest Research and Cooperation for Sustainable Development, Curitiba, Brazil 29 September – 5 October 2019. Pesquisa Forestal Brasileira – Brazilian Journal of Forestry Research, Colombo, v. 39, e201902043. Abstract.
  • Toth, I.K.; Campbell, E.; Cahill, G.; Elphinstone, J.; Humphris, S.; Saddler, G.S.; Wale, S.; Watts, L.; Pritchard, L.; Harper, G. (2018) Population studies of Pectobacterium atrosepticum: How it’s shaping our view of seed-borne vs environmental sources of infection., Phytopathology, 108, S1.259. Abstract.
  • Green, S.; Cooke, D.E.L.; Marzano, M.; Purse, B.; Sharp, P.; Chapman, D.; Schlenzig, A.; Barbrook, J.; Pettit, T.; Pérez-Sierra, A.; Henricot, B.; Frederickson-Matika, D.; Valatin, G.; Dunn, M.; Pritchard, L.; Thorpe, P.; Barwell, L.; Clark, M. (2017) PHYTO-THREATS: A multi-disciplinary approach to address global threats from Phytophthora species., International Union of Forest Research Organizations (IUFRO) 125th Anniversary Congress, Freiburg, Germany, 18-22 September 2017. (Poster)
  • Pritchard, L.; Humphris, S.; Saddler, G.; Parkinson, N.; Bertrand, V.; Elphinstone, J.; Toth, I. (2014) A new method of generating diagnostic primers from draft bacterial genome sequences., European Food Safety Authority (EFSA), Parma, 1-3 April 2014.
  • Brennan, F.P.; Pritchard, L.; Holden, N.M.; Abram, F. (2014) Exploring the genomic and phenotypic basis for E.coli naturalisation in soil., In: Cooperative of Zoonoses Experience and Expertise (CoZEE) Conference: The Role of High-throughput Sequencing in Surveillance, Diagnostics and Tracking Zoonotic Bacteria, The James Hutton Institute, Dundee, 11-12 November 2014.
  • Pritchard, L.; Bayer, M.; Cock, P.; Flores, P.; Jones, S.; Milne, I.; Shaw, P.; Marshall, D. (2014) James Hutton Institute Bioinformatics Grouping., Data Science Research Day, University of Edinburgh, 12 September 2014.
  • Pritchard, L.; Toth, I.K.; Humphris, S. (2013) Dickeya comparative metabolism., 14th International Conference on Systems Biology, Copenhagen, Denmark, 29 August – 4 September 2013.
  • Hein, I.; Gilroy, E.; Hornyik, C.; Bryan, G.; Milne, I.; Toth, I.K.; Ducreux, L.; Torrance, L.; Milne, L.; Cock, P.; Pritchard, L.; Sharma, K.; MacFarlane, S.; Zhang, R.; Hedley, P.; Jones, J.; Birch, P.; Taylor, M.; Dale, F.; McNaughton, I.; Wright, J.; Prashar, A.; Blok, V.; Carnegie, P.; Chapman, S. (2013) Utilising the potato genome., Potatoes in Practice 2013, Balruddery Farm, Invergowrie, Dundee, 8 August 2013.
  • Birch, P.R.J.; Boevink, P.C.; Gilroy, E.M.; Hein, I.; Pritchard, L.; Whisson, S.C. (2012) Effectors from the potato late blight pathogen: their roles in suppressing or triggering the plant immune system., EPS Autumn-school, Wageningen, 6 March 2012.
  • Birch, P.R.J.; Boevink, P.C.; Gilroy, E.M.; Hein, I.; Pritchard, L.; Randall, E.; Whisson, S.C. (2011) Effectors from the potato late blight pathogen: their roles in suppressing or triggering the plant immune system., British Mycological Society Meeting, Exeter, September 2011.
  • Gilroy, E.M.; Breen, S.; Morales, J.G.; Lokossou, A.A.; Ramos, B.; Armstrong, M.R.; Hein, I.; Boevink, P.; Pritchard, L.; van der Vossen, E.A.G.; Vleeshouwers, V.G.A.A.; Whisson, S.C.; Birch, P.R.J. (2009) Cloning and functional analysis of Phytophthora infestans RXLR effector, Avr2., 22nd New Phytologist Symposium on Effectors in Plant-Microbe Interactions, INRA Versailles Research Centre, Paris, France, 13-16 September 2009 (Poster).
  • Armstrong, M.R.; Whisson, S.C.; Pritchard, L.; Bos, J.I.B.; Venter, E.; Avrova, A.O.; Rehmany, A.P.; Huang, S.; Kamoun, S.; Beynon, J.; Birch, P.R.J. (2005) An ancestral oomycete locus contains late blight avirulence gene Avr3a, encoding a protein that is recognised in the host cell cytoplasm., Molecular Plant Microbe Interactions Conference, Merida, Mexico, 14-19 December 2005 (Poster).