Progress 09/15/04 to 08/31/08
Outputs
OUTPUTS: Shotgun Sanger sequencing of DNA from strain Emoy2 was completed to a depth of 8-fold coverage by Washington University genome sequencing center. An assembly of these sequences (called version 1) was made available to project members for review on February 17, 2006. WUGSC released assembly version 2.0 on their website and on VBI's website (vmd.vbi.vt.edu), incorporating Sanger Center (UK) BAC end sequences March 7, 2006. Fosmid end sequencing was completed by WUGSC and added to form assembly v3.0, which was released publicly July 12, 2007. Pre-finishing of the genome by Washington University was completed November 28, 2007, resulting in public release of annotated version 6.0 in March 2008. A further assembly including all BAC end sequence data from the Sanger Centre, but excluding EST data was completed Aug 11 2008 by Washington University. and publicly released as version 7.0 Aug 11 2008. A further version (7.1) is being completed by our collaborators in the UK that includes sequences of 98 BACs and 10 Mb of Illumina sequences. The availability of the sequence has been advertised through the Oomycete Genomics Research Collaboration Network Annual Meetings, on its website and via its email list. A genome sequence annotation jamboree was held on August 13-17, 2007 at the Virginia Bioinformatics in which 31 individuals participated, including 13 graduate students and 7 postdoctoral fellows. The genome sequence was also studied during oomycete comparative genomics mini-jamborees held at VBI on July 16-18, 2008 (31 attendees, including 8 undergraduates, 13 graduate students and 3 postdoctoral fellows, and 5 faculty from undergraduate institutions) and June 3-5, 2009 (40 participants including 15 graduate students, 7 postdoctoral fellows, plus 13 undergraduate students and 2 faculty from predominantly undergraduate institutions). PARTICIPANTS: INDIVIDUALS Brett M. Tyler (Professor, VT) Lead-PI. Overall project direction. Coordination of paper writing. John McDowell (Associate Professor), co-PI. Assists with overall project direction and coordination of paper writing. Provides H. arabidopsidis spores for DNA and RNA extraction. Marcus Chibucos (Postdoctoral Fellow) 50% effort. Annotation of the H. arabidopsidis genome sequence. Sucheta Tripathy (Senior Research Associate) 30% effort. Gene prediction and annotation from the genome sequence. Sandra Clifton (Washington University Genome Sequencing Center) Overall direction of sequencing efforts. PARTNER ORGANIZATIONS Washington University Genome Sequencing Center (Sandra Clifton). Funded collaborator. responsible for random shotgun sequencing using Sanger technology and sequence assembly. Warwick University, United Kingdom (Jim Beynon and Laura Baxter). With own funding provided BAC and EST sequences. The Wellcome Trust Sanger Institute, United Kingdom (Jane Rogers). With UK funding, produced BAC and EST sequences. The Sainsbury Institute, United Kingdom (Jonathan Jones). With funding from this award, produced cDNA sequencing using Illumina technology. With own funding, produced genome sequences using Illumina technology. Using own funding jointly analyzed Illumina and Sanger sequences. Utrecht University, Netherlands (guido van den Ackerveken). With own funding provided EST and proteomics data and functional genomics analysis. The Broad Institute (Rays Jiang). With own funds analyzed the effector repertoire of the H. arabidopsidis predicted proteome. COLLABORATORS AND CONTACTS All members of the Oomycete Genomics Research Collaboration Network, listed at http://pmgn.vbi.vt.edu/. TRAINING OR PROFESSIONAL DEVELOPMENT Three genome sequence analysis workshops were held which provided extensive opportunities for faculty, postdoctoral fellows, graduate students and undergraduate students. A genome sequence annotation jamboree was held on August 13-17, 2007 at the Virginia Bioinformatics in which 31 individuals participated, including 13 graduate students and 7 postdoctoral fellows. The genome sequence was also studied during oomycete comparative genomics mini-jamborees held at VBI during July 16-18, 2008 (31 attendees, including 8 undergraduates, 13 graduate students and 3 postdoctoral fellows, and 5 faculty from undergraduate institutions) and during June 3-5, 2009 (40 participants including 15 graduate students, 7 postdoctoral fellows, plus 13 undergraduate students and 2 faculty from predominantly undergraduate institutions). TARGET AUDIENCES: The target audience for this sequence is the international oomycete genomics research community. The availability of the sequence to this community has been advertised through the Oomycete Genomics Research Collaboration Network Annual Meetings, on its website and via its email list. Through NSF funding, this network provides training for members to learn how to analyze the sequence through travel awards to its annual meeting, training internships, and hosting of oomycete bioinformatics workshops, with an emphasis in each case on attendance by participants from minority-serving institutions, EPSCOR state institutions and from predominantly-undergraduate institutions, and by students, postdoctoral fellows, and minority researchers. A genome sequence annotation jamboree was held on August 13-17, 2007 at the Virginia Bioinformatics in which 31 individuals participated, including 13 graduate students and 7 postdoctoral fellows. The genome sequence was also studied during oomycete comparative genomics mini-jamborees held at VBI on July 16-18, 2008 (31 attendees, including 8 undergraduates, 13 graduate students and 3 postdoctoral fellows, and 5 faculty from undergraduate institutions) and June 3-5, 2009 (40 participants including 15 graduate students, 7 postdoctoral fellows, plus 13 undergraduate students and 2 faculty from predominantly undergraduate institutions). PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Comparison of the genome of HYALOPERONOSPORA ARABIDOPSIDIS (an obligate biotroph) with recently sequenced genomes of three PHYTOPHTHORA species (all saprotrophs) provided an opportunity to understand how an obligate biotroph has evolved from a free-living ancestor that employed a very different pathogenicity strategy. Our comparisons revealed two striking themes. First, gene families encoding proteins with potential to damage host cells or otherwise trigger defense responses (cell wall-degrading enzymes, elicitins, necrosis-inducing proteins, RxLR effectors, and others) are dramatically reduced in H. ARABIDOPSIDIS compared to PHYTOPHTHORA, indicative of optimization for stealth inside the host. Second, genes involved in several metabolic pathways were absent from H. ARABIDOPSIDIS, suggestive of metabolic dependency on the host. Some features of the H. ARABIDOPSIDIS gene space (maintenance of large numbers of secreted effectors, reduction in cell wall-degrading enzymes) are paralleled in the genomes of non-obligate, biotrophic fungi (the plant smut pathogen USTILAGO MAYDIS and the ectomycorrhizal symbiont LACCARIA BICOLOR), demonstrating that oomycetes and fungi have evolved similar molecular adaptations to a biotrophic lifestyle even though these lineages evolved independently from one another.
Publications
- Win, J., Morgan, W., Bos, J., Krasileva, K.V., Cano, L.M., Chaparro-Garcia, A., Ammar, R., Staskawicz, B.J., and Kamoun, S. (2007). Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes. Plant Cell 19, 2349-2369.
- Grouffaud, S., van West, P., Avrova, A.O., Birch, P.R., and Whisson, S.C. (2008). Plasmodium falciparum and Hyaloperonospora parasitica effector translocation motifs are functional in Phytophthora infestans. Microbiology (Reading, England) 154, 3743-3751.
- Dou, D., Kale, S.D., Wang, X., Jiang, R.H.Y., Bruce, N.A., Arredondo, F.D., Zhang, X., and Tyler, B.M. (2008). RXLR-mediated entry of Phytophthora sojae effector Avr1b into soybean cells does not require pathogen-encoded machinery. Plant Cell 20, 1930-1947.
- Dou, D., Kale, S.D., Wang, X., Chen, Y., Wang, Q., Wang, X., Jiang, R.H.Y., Arredondo, F.D., Anderson, R., Thakur, P., McDowell, J., Wang, Y., and Tyler, B.M. (2008). Carboxy-terminal motifs common to many oomycete RXLR effectors are required for avirulence and suppression of BAX-mediated programmed cell death by Phytophthora sojae effector Avr1b. Plant Cell 20, 1118-1133.
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