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

By Brian J. Haas, Sophien Kamoun, M. Zody, R. Jiang, Robert E. Handsaker, L. Cano, Manfred G. Grabherr, C. Kodira, S. Raffaele, T. Torto-Alalibo and 86 more. Nature, 2009

1,454 citations recorded by the source corpus.

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 ∼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 ∼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.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/4374b7439d505f85f4200780569831dcf857e5a3

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Citations in the corpus

Discovery of dark matter fungi in aquatic ecosystems demands a reappraisal of the phylogeny and ecology of zoosporic fungi (2016, positive): “Further, it might be possible to identify obligate fungal parasitism by analyzing genome-wide patterns of parasitism-relevant genes in order to search for a “two-speed genome”, analogous to what has been done for the Oomycete plant pathogen Phytophthora infestans (Haas et al., 2009).”
Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes (2013, background): “Some of them are devastating crop pathogens, such as Phytophthora infestans causing late blight of potato (Haas et al., 2009), but others include pathogens of fishes and algae, such as the water mold Saprolegnia parasitica causing diseases in fishes (Kale and Tyler, 2011) and Eurychasma dicksonii…”
Genome evolution in fungal plant pathogens: looking beyond the two-speed genome model (2020, positive): “Genes localized in repeat-rich and gene-sparse regions tend to evolve faster, in contrast to slow-evolving housekeeping genes localized in repeat-poor and gene-rich regions (Dong et al. , 2015; Haas et al. , 2009; Raffaele et al. , 2010; Raffaele and Kamoun, 2012).”
The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes (2012, result): “According to the present results and previous data on plant symbiotic and pathogenic fungi and oomycetes it seems that most TE-rich fungi interact with living plants (35-38).”
Obligate biotrophy features unraveled by the genomic analysis of rust fungi (2011, background): “Although proliferation of TEs might have contributed to the expansion of gene families in rust fungi, no specific localization of particular gene families was identified in TE-rich regions of rust genomes, such as reported for effectors in other plant pathogens (17,18, 19) (SI Text, Multigene Famili”
Advances in plant disease and pest management (2010, neutral): “Draft genomes can be accessed for many more species, including two nematodes and six Oomycetes (Stramenopiles), among them the causal agents of potato blight (Haas et al. 2009) and sudden oak death.”
Of PAMPs and Effectors: The Blurred PTI-ETI Dichotomy[OA] (2011, background): “…1 (Nep1)-like proteins that are conserved among bacteria, fungi, and oomycetes (Gijzen and Nürnberger, 2006; Kamoun, 2006), crinklers that are produced by oomycete species (Torto et al., 2003; Haas et al., 2009), and harpins that are produced byGram-negative bacteria (Tampakaki et al., 2010).”