Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire.
BACKGROUND
Pythium ultimum is a ubiquitous oomycete plant pathogen responsible for a variety of diseases on a broad range of crop and ornamental species.


RESULTS
The P. ultimum genome (42.8 Mb) encodes 15,290 genes and has extensive sequence similarity and synteny with related Phytophthora species, including the potato blight pathogen Phytophthora infestans. Whole transcriptome sequencing revealed expression of 86% of genes, with detectable differential expression of suites of genes under abiotic stress and in the presence of a host. The predicted proteome includes a large repertoire of proteins involved in plant pathogen interactions, although, surprisingly, the P. ultimum genome does not encode any classical RXLR effectors and relatively few Crinkler genes in comparison to related phytopathogenic oomycetes. A lower number of enzymes involved in carbohydrate metabolism were present compared to Phytophthora species, with the notable absence of cutinases, suggesting a significant difference in virulence mechanisms between P. ultimum and more host-specific oomycete species. Although we observed a high degree of orthology with Phytophthora genomes, there were novel features of the P. ultimum proteome, including an expansion of genes involved in proteolysis and genes unique to Pythium. We identified a small gene family of cadherins, proteins involved in cell adhesion, the first report of these in a genome outside the metazoans.


CONCLUSIONS
Access to the P. ultimum genome has revealed not only core pathogenic mechanisms within the oomycetes but also lineage-specific genes associated with the alternative virulence and lifestyles found within the pythiaceous lineages compared to the Peronosporaceae.
Lévesque
C André
CA
Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada.
Brouwer
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Cano
Liliana
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Hamilton
John P
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Carson
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Huitema
Edgar
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Raffaele
Sylvain
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Robideau
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Thines
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Zerillo
Marcelo M
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Busam
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Ferriera
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Fuerstenberg
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Gaulin
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Hostetler
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Johnson
Justin
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Krajaejun
Theerapong
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Lin
Haining
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Meijer
Harold J G
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Moore
Barry
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Morris
Paul
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Phuntmart
Vipaporn
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Puiu
Daniela
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Shetty
Jyoti
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Stajich
Jason E
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Tripathy
Sucheta
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Wawra
Stephan
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van West
Pieter
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Whitty
Brett R
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Pedro M
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Martin
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D000935:Antifungal Agents / Q000494:pharmacology; D001483:Base Sequence; D015820:Cadherins / Q000235:genetics; D050260:Carbohydrate Metabolism / Q000187:drug effects / Q000235:genetics; D023061:Gene Order / Q000235:genetics; D015321:Gene Rearrangement / Q000235:genetics; D016678:Genome / Q000235:genetics*; D054629:Genome, Mitochondrial / Q000235:genetics; D023281:Genomics; D054884:Host-Pathogen Interactions / Q000187:drug effects / Q000235:genetics; D006801:Humans; D005810:Multigene Family / Q000235:genetics; D010802:Phylogeny; D010944:Plants / Q000382:microbiology*; D011506:Proteins / Q000235:genetics* / Q000378:metabolism; D011775:Pythium / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development / Q000472:pathogenicity*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D026801:Synteny / Q000235:genetics
D000935:Antifungal Agents; D015820:Cadherins; D011506:Proteins