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Genome analyses of an aggressive and invasive lineage of the Irish potato famine pathogen.

TitleGenome analyses of an aggressive and invasive lineage of the Irish potato famine pathogen.
Publication TypeJournal Article
2012
AuthorsCooke, DEL, Cano, LM, Raffaele, S, Bain, RA, Cooke, LR, Etherington, GJ, Deahl, KL, Farrer, RA, Gilroy, EM, Goss, EM, Grünwald, NJ, Hein, I, MacLean, D, McNicol, JW, Randall, E, Oliva, RF, Pel, MA, Shaw, DS, Squires, JN, Taylor, MC, Vleeshouwers, VGAA, Birch, PRJ, Lees, AK, Kamoun, S
JournalPLoS Pathog
Volume8
Issue10
Paginatione1002940
Date Published2012
ISSN1553-7374
Crops, Agricultural, DNA Copy Number Variations, Gene Expression Profiling, Genes, Plant, Genome, Fungal, Host-Pathogen Interactions, Immunity, Innate, phytophthora infestans, Plant Diseases, Plant Proteins, Polymorphism, Genetic, Sequence Analysis, DNA, solanum tuberosum

<p>Pest and pathogen losses jeopardise global food security and ever since the 19(th) century Irish famine, potato late blight has exemplified this threat. The causal oomycete pathogen, Phytophthora infestans, undergoes major population shifts in agricultural systems via the successive emergence and migration of asexual lineages. The phenotypic and genotypic bases of these selective sweeps are largely unknown but management strategies need to adapt to reflect the changing pathogen population. Here, we used molecular markers to document the emergence of a lineage, termed 13_A2, in the European P. infestans population, and its rapid displacement of other lineages to exceed 75% of the pathogen population across Great Britain in less than three years. We show that isolates of the 13_A2 lineage are among the most aggressive on cultivated potatoes, outcompete other aggressive lineages in the field, and overcome previously effective forms of plant host resistance. Genome analyses of a 13_A2 isolate revealed extensive genetic and expression polymorphisms particularly in effector genes. Copy number variations, gene gains and losses, amino-acid replacements and changes in expression patterns of disease effector genes within the 13_A2 isolate likely contribute to enhanced virulence and aggressiveness to drive this population displacement. Importantly, 13_A2 isolates carry intact and in planta induced Avrblb1, Avrblb2 and Avrvnt1 effector genes that trigger resistance in potato lines carrying the corresponding R immune receptor genes Rpi-blb1, Rpi-blb2, and Rpi-vnt1.1. These findings point towards a strategy for deploying genetic resistance to mitigate the impact of the 13_A2 lineage and illustrate how pathogen population monitoring, combined with genome analysis, informs the management of devastating disease epidemics.</p>

10.1371/journal.ppat.1002940
Citation Key385
PubMed ID23055926
PubMed Central IDPMC3464212
Grant ListBB/E007120/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
BB/G015244/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
/ / Biotechnology and Biological Sciences Research Council / United Kingdom