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Phytophthora infestans


Phytophthora infestans is a devastating pathogen of critical food crops, causing late blight of potato and tomato. It is notorious as the causal agent of the Irish Potato Famine more than 150 years ago, and the crop losses due to P. infestans remain staggering today [2]. Worldwide losses in potato production alone caused by late blight exceed $5 billion annually, making P. infestans the single most important biotic threat to global food security [3,4]. In recent years, severe late blight epidemics occurred following the migration to North America, Europe and other regions of aggressive mating type strains [5,6,7]. Strategies for managing late blight remain unsustainable and costly and most populations are now resistant to previously effective fungicides [4,5,8,9,10]. As a result of the destruction caused by P. infestans, in 2003 The American Phytopathological Society ranked it among the Immediate Priority fungal and oomycete genome sequencing targets. In 2002 the same group had ranked P. infestans #2 among 26 fungal and oomycete species. The first ranked organism on that list, Magnaporthe grisea, has since been sequenced at the Broad Institute.

The oomycetes

P. infestans belongs to the oomycetes, a diverse group of deeply branching eukaryotic microorganisms that includes pathogens of plants, insects, crustaceans, fish, vertebrate animals, and microbes [11,12]. The diseases caused by these pathogens are notoriously difficult to manage on thousands of crop and ornamental plants, resulting in tens of billions of dollars of losses annually [2]. Because of their filamentous growth habit, oomycetes had been traditionally classified in the kingdom of fungi. In fact, modern molecular and biochemical analyses suggest that oomycetes have little taxonomic affinity with filamentous fungi, and are very distant in evolutionary terms from fungi, animals and plants. Rather, they are more closely related to brown algae (heterokonts) and diatoms in the Stramenopiles, one of several less well studied eukaryotic kingdoms [12,13,14].

Genome Facts

The genome size of P. infestans is estimated to be 237 Mb [15] (preliminary assembly data suggest it is slightly larger, 240-245 Mb). Two independent analyses indicate that the genome has about 52% GC content. Microscopic analyses indicate that P. infestans has 8-10 chromosomes [16]. Several studies suggest that genes are often tightly clustered in Phytophthora genomes [11,17,18].

Choice of Strain

T30-4 is an F1 of two aggressive strains of P. infestans originally isolated from potato in the Netherlands, and is considered the reference isolate for most genetic studies. This isolate was selected by the PIs after consultation with members of the P. infestans community. Significant resources have been generated in this strain: (1) a well characterized large insert BAC library has been constructed [19] and is available for use in this project; (2) it originates from the cross that was used to construct a genetic map based on AFLP markers [20] and that will be used for high density mapping in this project; and (3) it was the source for the 1X draft genome sequence produced previously by Syngenta [1].


  1. Randall, T.A., et al. (2005) Large-Scale Gene Discovery in the Oomycete Phytophthora infestans Reveals Likely Components of Phytopathogenicity Shared with True Fungi. Mol Plant Microbe Interact. 18: 229-243.
  2. Erwin, D.C. and Ribeiro, O.K. (1996). Phytophthora Diseases Worldwide. St. Paul, Minnesota, APS Press.
  3. Anonymous (1996). Late blight: A global initiative. Lima, Peru, International Potato Center (CIP).
  4. Duncan, J.M. (1999). Phytophthora-an abiding threat to our crops. Microbiol. Today 26:114-116.
  5. Fry, W.E. and Goodwin, S.B. (1997). Resurgence of the Irish potato famine fungus. Bioscience 47:363-371.
  6. Fry, W.E. and Goodwin, S.B. (1997). Re-emergence of potato and tomato late blight in the United States. Plant Dis. 81:1349-1357.
  7. Goodwin, S.B. and Fry, W.E. (1994). Genetic analyses of interspecific hybrids between Phytophthora infestans and Phytophthora mirabilis. Exp. Mycol. 18:20-32.
  8. Smart, C.D. and Fry, W.E. (2001). Invasions by the late blight pathogen: renewed sex and enhanced fitness. Biol. Invas. 3:235-243.
  9. Shattock, R.C. (2002). Phytophthora infestans: populations, pathogenicity and phenylamides. Pest Manag. Sci. 58:944-950.
  10. Ristaino, J.B. (2002). Tracking historic migrations of the Irish potato famine pathogen, Phytophthora infestans. Microbes Infect. 4:1369-1377.
  11. Kamoun, S. (2003). Molecular genetics of pathogenic oomycetes. Eukaryotic Cell 2:191-199.
  12. Margulis, L. and Schwartz, K.V. (2000). Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth. New York, W.H. Freeman and Co.
  13. Baldauf, S.L., et al. (2000). A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290:972-977.
  14. Sogin, M.L. and Silberman, J.D. (1998). Evolution of the protists and protistan parasites from the perspective of molecular systematics. Int. J. Parasitol. 28:11-20.
  15. Tooley, P.W. and Therrien, C.D. (1987). Cytophotometric determination of the nuclear DNA content of 23 Mexican and 18 non-Mexican isolates of Phytophthora infestans. Exp. Mycol. 11:19-26.
  16. Sansome, E. and Brasier, C.M. (1973). Diploidy and chromosomal structural hybridity in Phytophthora infestans. Nature 241:344-345.
  17. Randall, T.A., et al. (2003). Chromosomal heteromorphism and an apparent translocation detected using a BAC contig spanning the mating type locus of Phytophthora infestans. Fungal Genet Biol. 38:75-84.
  18. Cvitanich, C. and Judelson, H.S. (2003). Stable transformation of the oomycete, Phytophthora infestans, using microprojectile bombardment. Curr Genet. 42:228-235.
  19. Whisson, S.C., et al. (2001). Physical mapping across an avirulence locus of Phytophthora infestans using a highly representative, large-insert bacterial artificial chromosome library. Mol. Genet. Genomics 266:289-295.
  20. van der Lee, T., Testa, A., Robold, A., van 't Klooster, J.W. and Govers, F. (2004) High density genetic linkage maps of Phytophthora infestans reveal trisomic progeny and chromosomal rearrangements. Genetics 167, 111-129.