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United States Department of Agriculture

Agricultural Research Service

Title: What Can Availability of the Phytophthora ramorum Genome Do for Us?

Author
item Grunwald, Niklaus

Submitted to: Sudden Oak Death Science Symposium
Publication Type: Proceedings
Publication Acceptance Date: September 12, 2007
Publication Date: March 15, 2008
Citation: Grunwald, N.J. 2008. What can availability of the Phytophthora ramorum genome do for us?. Sudden Oak Death Science Symposium. p.233-238.

Technical Abstract: The complete genomes of Phytophthora ramorum and P. sojae were sequenced in 2004. Two obvious questions arise, What contributions does the availability of a genome sequence make toward understanding the biology of Phytophthora spp.? What are the implications for management of sudden oak death in the field? Simultaneous sequencing of two Phytophthora genomes allowed for direct comparison of similarities and differences between these two organisms. Of the 19,027 predicted genes in P. sojae and 15,743 gene models in P. ramorum, 9,768 are predicted to have the same function. These two genomes both revealed a rapid expansion and diversification of many protein families associated with plant infection including different classes of pathogen effectors. Pathogen effectors can serve a virulence function on behalf of the pathogen or trigger a rapid defense response in resistant hosts. Two protein motifs (RxLR and dEER) are shared by the four known effectors in plant pathogenic oomycetes. Genome analyses identified a diverse superfamily of approximately 350 genes in P. ramorum that share these motifs. These have been termed avirulence homolog genes. With these sequences in hand, we were able to clone homologous Avh loci from sister-taxa P. lateralis and P. hibernalis. Availability of the P. ramorum genome sequence has also resulted in several practical applications. We have, for instance, started to investigate which genes are differentially expressed during different life-stages (mycelium, zoospores, etc.) and during plant infection using microarrays developed from the current genome annotation. The genome has been mined for molecular loci that can be used for pathogen identification and genotyping. The genomes have been helpful in selecting sequence loci that can be used for constructing a phylogeny of the genus Phytophthora. The genome has also been helpful in finding simple sequence repeats and sequence loci that have been used to study the population structure and migration of clones.

Last Modified: 10/21/2014
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