- ORCID ID: 0000-0002-8392-2822
- ResearcherID: A-7331-2008
- Scopus ID: 8581614700
- Google Scholar: 5QhdsWkAAAAJ
Current research interests
- Computational biology and bioinformatics.
- Oomycete and bacterial plant pathogens.
- Systems biology of plant-pathogen interactions.
- Comparative genomics of plant pathogens.
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.
- 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
Sequenced genomes provide an opportunity for comparative genomics to determine which features might confer particular functions and behaviours on an organism. Sequence annotation also remains a challenge, even for well-studied organisms. I use computational and machine-learning approaches to aid classification of genome features and identify features that may be associated with the ability of a microbe to cause disease.
Phytophthora infestans (Haas et al. 2009), Pectobacterium atrosepticum (Bell et al. 2004), and Dickeya spp. (Pritchard et al. 2013) genome sequencing. Comparative genomics of plant pathogens (Toth et al. 2006), including microarray comparative genomic hybridisation (Pritchard et al. 2009). Identification and classification of pathogen effectors and their targets (McLellan et al. 2013, McNally et al. 2012, Whisson et al. 2007, Haas et al. 2009) and other genomic features (Jupe et al. 2013, Jupe et al. 2012, Avrova et al. 2007, Kikuchi et al. 2007, Whisson et al. 2005, Bell et al. 2004). Diagnostic assays from rough draft genome sequences (Pritchard et al. 2012, Pritchard et al. 2013).
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. 2012, Antunez-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)
- 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.
- Jupe F, Witek K, Verweij W, Sliwka J, Pritchard L, et al. 2013 Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations. The Plant Journal 76: 530–544. (doi:10.1111/tpj.12307)
- Mclellan H, Boevink PC, Armstrong MR, Pritchard L, Gomez S, et al. 2013 An RxLR Effector from Phytophthora infestans Prevents Re-localisation of Two Plant NAC Transcription Factors from the Endoplasmic Reticulum to the Nucleus. PLoS Pathogens 9: e1003670. (doi:10.1371/journal.ppat.1003670)
- Milne I, Stephen G, Bayer M, Cock PJA, Pritchard L, et al. 2013 Using Tablet for visual exploration of second-generation sequencing data. Briefings in Bioinformatics 14: 193–202. (doi:10.1093/bib/bbs012)
- Cock PJA, Grüning BA, Paszkiewicz K, Pritchard L 2013 Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology. PeerJ 1: e167. (doi:10.7717/peerj.167)
- Pritchard L, Humphris S, Saddler GS, Parkinson NM, Bertrand V, et al. 2013 Detection of phytopathogens of the genus Dickeya using a PCR primer prediction pipeline for draft bacterial genome sequences. Plant Pathology 62: 587–596. (doi:10.1111/j.1365-3059.2012.02678.x)
- Pritchard L, Humphris S, Baeyen S, Maes M, Van Vaerenbergh J, et al. 2013 Draft Genome Sequences of Four Dickeya dianthicola and Four Dickeya solani Strains. Genome Announcements 1. (doi:10.1128/genomeA.00087-12)
- Pritchard, L., Holden, N.J., Bielaszewska, M., Karch, H., Toth, I.K. 2012 Alignment-Free Design of Highly Discriminatory Diagnostic Primer Sets for Escherichia coli O104:H4 Outbreak Strains. PLoS ONE 7: e34498.(doi:10.1371/journal.pone.0034498)
- Rio-Alvarez, I., Rodríguez-Herva, J.J., Cuartas-Lanza, R., Toth, I., Pritchard, L., et al. 2012 Genome-Wide Analysis of the Response of Dickeya dadantii 3937 to Plant Antimicrobial Peptides. Mol Plant Microbe Interact 25: 523–533. (doi:10.1094/MPMI-09-11-0247)
- Jupe, F., Pritchard, L., Etherington, G.J., Mackenzie, K., Cock, P.J., Wright, F., Sharma, S.K., Bolser, D., Bryan, G.J., Jones, J.D., Hein, I. 2012. Identification and localisation of the NB-LRR gene family within the potato genome. BMC Genomics 2012 13:75. (doi:10.1186/1471-2164-13-75)
- McNally, R.R., Toth, I.K., Cock, P.J.A., Pritchard, L., Hedley, P.E., Morris, J.A., Zhao, Y., Sundin, G.W. 2012 Genetic characterization of the HrpL regulon of the fire blight pathogen Erwinia amylovora reveals novel virulence factors. Mol Plant Pathol 13: 160–173. (doi:10.1111/j.1364-3703.2011.00738.x)
- Gilroy, E.M., Breen, S., Whisson, S.C., Squires, J., Hein, I., Kaczmarek, M., Turnbull, D., Boevink, P.C., Lokossou, A., Cano, L.M., Morales, J., Avrova, A.O., Pritchard, L., Randall, E., Lees, A., Govers, F., van West, P., Kamoun, S., Vleeshouwers, V.G., Cooke, D.E., Birch, P.R. 2011. Presence/absence, differential expression and sequence polymorphisms between PiAVR2 and PiAVR2-like in Phytophthora infestans determine virulence on R2 plants. New Phytologist 2011 191:3 763-776 (doi: 10.1111/j.1469-8137.2011.03736.x)
- Pritchard L., Birch P.R. 2011 A systems biology perspective on plant-microbe interactions: Biochemical and structural targets of pathogen effectors. Plant Science180: 584-603. doi:10.1016/j.plantsci.2010.12.008.
- Antunez-Lamas,M., Cabrera, E, Lopez-Solanilla, E., Solano, R., González-Melendi, P., Chico, J.M., Toth, I.K., Birch, P.R.J., Pritchard, L., Liu, H., and Rodriguez-Palenzuela, P. 2009. Bacterial chemoattraction towards jasmonate plays a role in the entry of Dickeya dadantii through wounded tissues. Molecular Microbiology 74(3), 662-671. (doi:10.1111/j.1365-2958.2009.06888.x)
- Haas, B.J., Kamoun, S., Zody, M.C., [+59 authors+] Pritchard, L. [+29 authors+] Birch, P.R.J., Whisson, S.C., Judelson, H.S. & Nusbaum, C. 2009. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature 461, 393-398. (doi:10.1038/nature08358)
- Pritchard, L., Liu, H., Booth, C., Douglas, E., Francois, P., Schrenzel, J., Hedley, P., Birch, P.R.J. and Toth, I.K. 2009. Microarray comparative genomic hybridisation analysis incorporating genomic organisation, and application to enterobacterial plant pathogens. PLoS Computational Biology 5(8), e1000473.
- Birch, P.R.J., Armstrong, M.A., Bos, J., Boevink, P.C., Gilroy, E.M., Taylor, R.M., Wawra, S., Pritchard, L., Conti, L.., Ewan, R., Whisson, S.C., van West, P., Sadanandom, A., and Kamoun, S. 2009. Towards understanding the virulence functions of RXLR effectors of the oomycete plant pathogen Phytophthora infestans. Journal of Experimental Botany 60, 1133-1140. (doi:10.1093/jxb/ern353)
- Holden, N., Pritchard, L. and Toth, I.K.. 2008. Colonization outwith the colon:plants as an alternative environmental reservoir for human pathogenic enterobacteria. FEMS Microbiology Reviews 33, 689-703. (doi:10.1111/j.1574-6976.2008.00153.x)
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