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

@article{Haas2009GenomeSA,
  title={Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans},
  author={Brian J. Haas and Sophien Kamoun and Michael C. Zody and Rays H. Y. Jiang and Robert E. Handsaker and Liliana M. Cano and Manfred G. Grabherr and Chinnappa D. Kodira and Sylvain Raffaele and Trudy A Torto-Alalibo and Tolga Osman Bozkurt and Audrey M. V. Ah-Fong and Lucia Alvarado and Victoria L. Anderson and Miles R Armstrong and Anna O. Avrova and Laura Baxter and Jim L. Beynon and Petra C. Boevink and Stephanie R. Bollmann and Jorunn Indra Berit Bos and Vincent Bulone and Guohong Cai and Cahid Cakir and James C. Carrington and M. Chawner and Lucio Conti and Stefano Costanzo and Richard A Ewan and N. Fahlgren and Michael A. Fischbach and Johanna Fugelstad and Eleanor M. Gilroy and Sante Gnerre and Pamela J. Green and Laura J. Grenville-Briggs and Jack Griffith and Niklaus J. Gr{\"u}nwald and K. Horn and Neil R. Horner and Chia-Hui Hu and Edgar Huitema and Dong-Hoon Jeong and Alexandra M. E. Jones and Jonathan D. G. Jones and Richard W. Jones and Elinor K. Karlsson and Sridhara G. Kunjeti and Kurt Lamour and Zhenyu Liu and Li‐Jun Ma and Daniel MacLean and Marcus C. Chibucos and Hayes McDonald and Jessica McWalters and Harold J. G. Meijer and William Morgan and Paul F. Morris and Carol A. Munro and Keith H. O'Neill and Manuel D. Ospina-Giraldo and Andr{\'e}s Pinz{\'o}n and L. Pritchard and Bernard H. Ramsahoye and Qinghu Ren and Silvia Restrepo and Sourav Roy and Ari Sadanandom and Alon Savidor and Sebastian Schornack and David C. Schwartz and Ulrike Schumann and Benjamin Schwessinger and Lauren A. Seyer and Ted Sharpe and Cristina Silvar and Jing Song and David J. Studholme and Sean M. Sykes and Marco Thines and P. van de Vondervoort and Vipaporn Phuntumart and Stephan Wawra and R. L. Weide and Joe Win and Carolyn A. Young and Shiguo Zhou and William E. Fry and Blake C. Meyers and Pieter van West and Jean Beagle Ristaino and Francine Govers and Paul R. J. Birch and Stephen C. Whisson and Howard S. Judelson and Chad Nusbaum},
  journal={Nature},
  year={2009},
  volume={461},
  pages={393-398}
}
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. [] Key Result 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.

Figures and Tables from this paper

Genome Analyses of an Aggressive and Invasive Lineage of the Irish Potato Famine Pathogen
TLDR
It is shown 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, illustrating how pathogen population monitoring, combined with genome analysis, informs the management of devastating disease epidemics.
Molecular Diagnosis of Killer Pathogen of Potato: Phytophthora infestans and Its Management
TLDR
This review examines the technical advances in the field and the rationale for such studies on Phytophthora and new technologies promise to improve the speed and accuracy of disease diagnostics and pathogen detection.
The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine
TLDR
It is proposed that HERB-1 and US-1 emerged from a metapopulation that was established in the early 1800s outside of the species' center of diversity, which replaced it outside of Mexico in the 20th century.
Evolution and Management of the Irish Potato Famine Pathogen Phytophthora Infestans in Canada and the United States
TLDR
Management of late blight will therefore require new, multifaceted strategies which include monitoring pathogen evolution and implementing sustainable production practices, as well as increased genetic diversity and pathogenicity.
Analysis of the lineage of Phytophthora infestans isolates using mating type assay, traditional markers, and next generation sequencing technologies
TLDR
To manage this disease, it is important to understand the genetic divergence of P. infestans isolates as well as breeding of resistant cultivars to facilitate the elimination of the late blight disease.
Analysis of the lineage of Phytophthora infestans isolates using mating type assay, traditional markers, and next generation sequencing technologies
TLDR
To manage this disease, it is important to understand the genetic divergence of P. infestans isolates as well as breeding of resistant cultivars to facilitate the elimination of the late blight disease.
The oomycete broad-host-range pathogen Phytophthora capsici.
TLDR
Phytophthora capsici presents an oomycete worst-case scenario to growers as it has a broad host range, often produces long-lived dormant sexual spores, has extensive genotypic diversity and has an explosive asexual disease cycle.
Reconstructing genome evolution in historic samples of the Irish potato famine pathogen
TLDR
At least one of these genotypes encodes a virulent phenotype in modern strains, which helps explain the 20th century’s episodic replacements of European P. infestans lineages.
The hidden duplication past of the plant pathogen Phytophthora and its consequences for infection
TLDR
The fact that many small blocks of duplicated genes are found indicates that the genomes of Phytophthora species have been heavily rearranged following the WGD, and the high repeat content in these genomes have played an important role in this rearrangement process.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 28 REFERENCES
An ancestral oomycete locus contains late blight avirulence gene Avr3a, encoding a protein that is recognized in the host cytoplasm.
TLDR
The oomycete Phytophthora infestans causes late blight, the potato disease that precipitated the Irish famines in 1846 and 1847, and it is suggested that Avr3a has undergone gene duplication and that an allele evading recognition by R3a arose under positive selection.
Effector Genomics Accelerates Discovery and Functional Profiling of Potato Disease Resistance and Phytophthora Infestans Avirulence Genes
TLDR
The findings indicate that effector genomics enables discovery and functional profiling of late blight R genes and Avr genes at an unprecedented rate and promises to accelerate the engineering ofLate blight resistant potato varieties.
Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis
TLDR
Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oömycete avirulence genes.
The Phytophthora infestans avirulence gene Avr4 encodes an RXLR-dEER effector.
TLDR
It is shown that expression of PiAvr4 in R4 plants using PVX agroinfection and agroinfiltration showed that PiAvR4 itself is the effector that elicits HR on R4 but not r0 plants, demonstrating that Pi Avr4 is responsible for eliciting R4-mediated resistance.
Societal Costs of Late Blight in Potato and Prospects of Durable Resistance Through Cisgenic Modification
TLDR
A case arguing for an updating and refinement of these rules in order to place cisgenic GM-crops in another class of GM-plants as has been done in the past with (induced) mutation breeding and the use of protoplast fusion between crossable species is presented.
A gene encoding a protein elicitor of Phytophthora infestans is down-regulated during infection of potato.
TLDR
The potential role of INF1 as an elicitor in interactions between P. infestans and Solanum species was investigated and it was shown to be expressed in mycelium grown in various culture media, whereas it was not expressed in sporangiospores, zoospore, cysts, and germinating cysts.
Phytophthora infestans: the plant (and R gene) destroyer.
  • W. Fry
  • Biology
    Molecular plant pathology
  • 2008
TLDR
Phytophthora infestans remains a problem to production agriculture and the plasticity of its genome as revealed in population diversity and in the abundance of putative effectors means that this oomycete remains a formidable foe.
A catalogue of the effector secretome of plant pathogenic oomycetes.
  • S. Kamoun
  • Biology
    Annual review of phytopathology
  • 2006
TLDR
This review classifies and catalogues the effector secretome of oomycetes, a phylogenetically distinct group of eukaryotic microorganisms that includes some of the most notorious pathogens of plants.
...
1
2
3
...