Pythium Genome Database

Pythium Genome Database

Manuscript published July 2010:

Lévesque et al., Genome sequence of the necrotrophic plant pathogen, Pythium ultimum, reveals original pathogenicity mechanisms and effector repertoire. Genome Biology 2010 11:R73 - view paper at Genome Biology


Agricultural production is under constant and increasing pressure from losses due to plant pathogens. One important and ubiquitous plant pathogen taxon is the genus Pythium, a fungal-like organism, which causes a variety of diseases including seed rots and damping-off, root, stem and fruit rots, foliar blights and postharvest decay.Pythium spp. are a major cause of seed rot prior to germination, especially in poorly drained soils and almost all germinating seeds and developing roots are exposed to infection by Pythium.

Oospore of Pythium ultimum with antheridium and fertilization tube.

Photo taken by Dr. Kanak Bala in the laboratory of André Lévesque

However, we currently have only a limited understanding on the molecular basis of its pathogenicity. More importantly, plant disease diagnosticians do not routinely identify Pythium to the species level because of the difficulty and time required to produce and identify the morphological characteristic necessary for speciation. While most Pythium species can be differentiated based on sequence differences in the ribosomal RNA internal transcribed spacer (ITS), in several cases, representative strains of one species had identical ITS sequences to those of another, thereby suggesting taxonomic synonymy among certain described species or the need for multigenic analysis to set species boundaries.

Pythium ultimum EST Sequencing

To gain a better understanding of the transcriptome of Pythium ultimum, we generated Expressed Sequence Tags (ESTs) from Pythium ultimum DAOM BR144 (=ATCC 200006 = CBS 805.95). RNA was isolated from nutrient-rich and nutrient-limiting grown hyphae and a normalized cDNA population was constructed. A total of 9,578 reads were generated using Sanger sequencing methods. The Sanger derived ESTs have been assembled into a Transcript Assembly and are available through the Comprehensive Phytopathogen Genome Resource Transcript Assemblies Project.

Pythium ultimum Whole Genome Sequencing

The American Phytopathological Society identified Pythium as one of the ‘high priority’ plant pathogens for microbial genome sequencing. We propose to increase our knowledge of this significant plant pathogen genus by sequencing and annotating Pythium genomes. The Pythium ultimum genome has already been sequenced and comparative analyses was performed with Phytophthora relatives. To further our understanding of the oomycetes, we sequenced genome sequence of six additional species of Pythium and performed comparative analyses with closely related oomycetes.

Pythium ultimum mature oospore

Photo taken by Dr. Kanak Bala in the laboratory of André Lévesque

Such data already exist for three Phytophthora species. Through these comparative analyses, we will be able to further our understanding of not only this important plant pathogen, but also how to develop more relevant diagnostic markers that can be used in detecting, controlling the dissemination, and limiting the impact of this plant pathogen and its relatives.

We will train a graduate student in genomics and bioinformatics and engage a number of outside scientists, including other graduate students and postdoctoral fellows, in annotation and comparative genomics of Pythium.

Additional Pythium Genome and Transcriptome Resources

We have also sequenced an additional six Pythium species to broaden the representation of genome and transcriptome sequences for this important genus. The following isolates were sequenced using next generation sequencing methods, assembled and annotated for gene content. Transcriptome sequences, in the form of RNA-seq data, were generated for five of the six species. Detailed descriptions of the sequencing and analysis of these genomes/transcriptomes are detailed in Adhikari et al. (under review) and Zerillo et al. (under review). Their sequences can be downloaded here.

SpeciesCBS accessionOther accession identifiers
Pythium aphanidermatum132490DAOM BR444
Pythium arrhenomanes324.62ATCC 12531
Pythium irregulare250.28DAOM BR486
Pythium iwayamai132417DAOM 242034
P. ultimum var. sporangiiferum219.65DAOM BR650
Pythium vexans119.80DAOM BR484

The Pythium ultimum EST Sequencing was supported by the USDA National Research Initiative Cooperative State Research Extension Education Service (grant 2006-55605-16645 and 2006-55605-04558)

The Pythium ultimum Whole Genome Sequencing was supported by the National Research Initiative of the USDA Cooperative State Research, Education and Extension Service, grant number 2007-35600-17774 and 2007-35600-18886.