Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans

Brian J Haas, Sophien Kamoun, Michael C Zody, Rays H Y Jiang, Robert E Handsaker, Liliana M Cano, Manfred Grabherr, Chinnappa D Kodira, Sylvain Raffaele, Trudy Torto-Alalibo, Tolga O Bozkurt, Audrey M V Ah-Fong, Lucia Alvarado, V Anderson, Miles R Armstrong, Anna Avrova, Laura Baxter, Jim Beynon, Petra C Boevink, Stephanie R BollmannJorunn I B Bos, Vincent Bulone, Guohong Cai, Cahid Cakir, James C Carrington, Megan Chawner, Lucio Conti, Stefano Costanzo, Richard Ewan, Noah Fahlgren, Michael A Fischbach, Johanna Fugelstad, Eleanor M Gilroy, Sante Gnerre, Pamela J Green, Laura Grenville-Briggs, John Griffith, Niklaus J Grünwald, Karolyn Horn, Neil R Horner, Chia-Hui Hu, Edgar Huitema, Dong-Hoon Jeong, Alexandra M E Jones, Jonathan D G Jones, Richard W Jones, Elinor K Karlsson, Sridhara G Kunjeti, Kurt Lamour, Zhenyu Liu, Lijun Ma, Daniel Maclean, Marcus C Chibucos, Hayes McDonald, Jessica McWalters, Harold J G Meijer, William Morgan, Paul F Morris, Carol A Munro, Keith O'Neill, Manuel Ospina-Giraldo, Andrés Pinzón, Leighton Pritchard, Bernard Ramsahoye, Qinghu Ren, Silvia Restrepo, Sourav Roy, Ari Sadanandom, Alon Savidor, Sebastian Schornack, David C Schwartz, Ulrike Schumann, Ben Schwessinger, Lauren Seyer, Ted Sharpe, Cristina Silvar, Jing Song, David J Studholme, Sean Sykes, Marco Thines, Peter J I van de Vondervoort, Vipaporn Phuntumart, Stephan W Wawra, Rob Weide, Joe Win, Carolyn Young, Shiguo Zhou, William Fry, Blake C Meyers, Pieter Van West, Jean Ristaino, Francine Govers, Paul R J Birch, Stephen C Whisson, Howard S Judelson, Chad Nusbaum

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Abstract

Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement. To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population. Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion. Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars. Here we report the sequence of the P. infestans genome, which at approximately 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for approximately 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.
Original languageEnglish
Pages (from-to)393-398
Number of pages6
JournalNature
Volume461
Issue number7262
Early online date9 Sep 2009
DOIs
Publication statusPublished - 17 Sep 2009

Keywords

  • algal proteins
  • DNA transposable elements
  • DNA, intergenic
  • evolution, molecular
  • genome
  • host-pathogen interactions
  • humans
  • Ireland
  • molecular sequence data
  • necrosis
  • phenotype
  • Phytophthora infestans
  • plant diseases
  • Solanum tuberosum
  • starvation

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    Haas, B. J., Kamoun, S., Zody, M. C., Jiang, R. H. Y., Handsaker, R. E., Cano, L. M., Grabherr, M., Kodira, C. D., Raffaele, S., Torto-Alalibo, T., Bozkurt, T. O., Ah-Fong, A. M. V., Alvarado, L., Anderson, V., Armstrong, M. R., Avrova, A., Baxter, L., Beynon, J., Boevink, P. C., ... Nusbaum, C. (2009). Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature, 461(7262), 393-398. https://doi.org/10.1038/nature08358