Source: VIRGINIA BIOINFORMATICS INSTITUTE submitted to
GENOME SEQUENCE OF PHYTOPHTHORA SOJAE
 
PROJECT DIRECTOR: Tyler, B. M. Sobral, B. W. Boore, J. L.
 
PERFORMING ORGANIZATION
(N/A)
VIRGINIA BIOINFORMATICS INSTITUTE
BLACKSBURG,VA 24060
 
NON TECHNICAL SUMMARY: Plant pathogens from the genus Phytophthora cause destructive diseases of an enormous variety of crop and non-crop plant species. Some of the most severely impacted crops include potato, tomato, soybean, cacao, citrus, walnut, avocado, pepper and cucurbits. Forests and native ecosystems have been devastated by broad host range Phytophthora species such as P. cinnamomi and the newly emerging pathogen of California's oak forests, P. ramorum. The potato pathogen P. infestans was responsible for the Irish potato famine in the 19th century. Superficially, Phytophthora pathogens resemble fungi, but they in fact belong to a group called oomycetes that are most closely related to algae such as kelp and diatoms. Hence conventional fungal control measures often fail against these pathogens. This project, which will also be funded by the National Science Foundation and the Department of Energy, will create a comprehensive genetic resource to assist the development of new Phytophthora disease control measures by creating a rough draft the entire DNA sequence of the soybean pathogen Phytophthora sojae. P. sojae is relatively easy to genetically manipulate, which will assist deciphering the functions of the genes encoded in the sequence, and in applying lessons from the sequence to other Phytophthora species. Comparison of the P. sojae sequence with a draft sequence of the oak sudden death pathogen P. ramorum, to be funded by the DOE, will yield further insights into mechanism of pathogenicity in Phytophthora species in general and in the oak disease pathogen specifically.
 
OBJECTIVES: 1. Sequence the genome of the oomycete plant pathogen Phytophthora sojae to a depth of 5fold 2. Assemble the P. sojae BAC library into contigs. 3. Assemble the sequence and carry out machine annotation. 4. Establish a bioinformatics platform for community finishing and annotation of the draft sequence,
 
APPROACH: Objective 1. Sequence will be determined by paired-end sequencing of 3-4 kb clones generated by physical shearing - a random shotgun strategy. Objective 2. BAC library will be assembled into contigs by using restriction enzyme fingerprinting, EST hybridization and repetitive sequence fingerprinting. Analysis will use FPC (FingerPrint Contig) software. Objective 3. Assembly will be by PHRAP with human verification. Annotation will include BLAST searches, gene finding and EST matching. Objective 4. Community annotation will be based on the ASAP (A Systematic Annotation Package) package developed by Nicole Perna (U. Wisconsin) which explicitly supports annotation of an evolving sequence.
 
CRIS NUMBER: 0193889 SUBFILE: CRIS
PROJECT NUMBER: VAR-2002-04334 SPONSOR AGENCY: CSREES
PROJECT TYPE: NRI COMPETITIVE GRANT PROJECT STATUS: TERMINATED MULTI-STATE PROJECT NUMBER: (N/A)
START DATE: Sep 15, 2002 TERMINATION DATE: Sep 14, 2004

GRANT PROGRAM: MICROBE SEQUENCING PROJECT
GRANT PROGRAM AREA: Plant Sciences

CLASSIFICATION
Knowledge Area (KA)Subject (S)Science (F)Objective (G)Percent
212182010404.2100%

CLASSIFICATION HEADINGS
KA212 - Pathogens and Nematodes Affecting Plants
S1820 - Soybean
F1040 - Molecular biology
G4.2 - Reduce Number and Severity of Pest and Disease Outbreaks


RESEARCH EFFORT CATEGORIES
BASIC 100%
APPLIED (N/A)%
DEVELOPMENTAL (N/A)%

KEYWORDS: phytophthora sojae; oomycetes; phytophthora; fungus genetics; genomes; dna sequences; soybeans; root rot (soybeans); sudden death syndrome; fungus diseases (plants); plant disease control; plant pathology; molecular genetics; libraries; artificial chromosomes; bacteria; bioinformatics; quercus; host range; gene function; plant genetics; pathogenicity

PROGRESS: Sep 15, 2002 TO Sep 14, 2004
A 9X random shotgun sequence of the 95 Mb genome of Phytophthora sojae and a 7X random shotgun sequence of the 65 Mb Phytophthora ramorum genome have been completed, assembled and annotated. The DOE JGI has made the sequence available at http://genome.jgi-psf.org. 14592 were subjected to restriction enzyme fingerprinting and assembled into a physical map of 257 BAC contigs. A minimum tile path of 1440 clones was selected and subjected to BAC-end sequencing in order to merge the genome sequence with the physical map. The merge resulted in a combined map consisting of 79 super-contigs. A community annotation database based on the Genome Unified Schema (GUS) was established and is available at http://phytophthora.vbi.vt.edu. Electronic annotation predicted 19,027 genes in P.sojae and 15,743 genes in P.ramorum. 9,768 putative pairs of orthologs were identified between the two species. 7,850 ESTs from P. sojae were used for validation, correction and extension of predicted gene models. Additional annotation has been provided by the Phytophthora research community via an Annotation Jamboree and the community gene annotation interface. Whole-genome DNA sequence alignment demonstrated a high level of similarity between the two species; 75.8% of all P. ramorum and 79.7% of all P. sojae exons were covered by the alignment. Based on single-linkage clustering analysis, the majority of predicted genes from both genomes form groups of homologous proteins. Only a small number of genes, 1,755 in P. sojae and 624 in P. ramorum, did not have a homolog in the other genome when a significance threshold of 1e-8 was used. The overall higher number of predicted genes in P. sojae results from greater expansion of many gene families in P. sojae. Overall, about 80% of the genes in both genomes have homology to known proteins or known protein domains. 1,563 pairs of Phytophthora orthologs showed no homology to any other species than Phytophthora. Analysis of the genes encoded in the genome sequences supports the hypothesis that heterotrophic Stramenopiles such as the oomycetes, and photosynthetic Stramenopiles such as diatoms share a secondarily photosynthetic ancestor. The genomes show rapid diversification of proteins associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors and avirulence gene products, but relatively little diversification of biosynthetic genes for metabolite toxins. The P. sojae and P. ramorum genomes show substantial gene colinearity (synteny) except in regions encoding putative pathogenicity genes, where there is evidence for accelerated genome evolution.

IMPACT: 2002-09-15 TO 2004-09-14 The genome sequences of Phytophthora sojae and Phytophthora ramorum provide many new insights into the mechanisms that these pathogens use to attack their host plants. These insights will aid in developing new methods for protecting plants against these pathogens. In addition the Phytophthora ramorum genome sequence has provided new tools for genetic identification and tracking of this forest and nursery pathogen.

PUBLICATION INFORMATION: 2002-09-15 TO 2004-09-14
Jiang, R.H.Y., Tyler, B.M., Whisson, S.C., Hardham, A.R. and Govers, F. 2006. Ancient origin of elicitin gene clusters in Phytophthora genomes. Mol. Biol. Evol., 23:in press.

PROJECT CONTACT INFORMATION
NAME: Tyler, B. M.
PHONE: 540-231-7318
FAX: 540-231-2606