Pacific Southwest

Title: What can availability of the Phytophthora ramorum genome do for us?

Author: Grünwald, Niklaus J.

Date: 2008

Source: In: Frankel, Susan J.; Kliejunas, John T.; Palmieri, Katharine M., tech. coords. 2008. Proceedings of the sudden oak death third science symposium. Gen. Tech. Rep. PSW-GTR-214. Albany, CA: U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station. pp. 233-238

Station ID: GTR-PSW-214

Description: The complete genomes of Phytophthora ramorum and P. sojae have recently been sequenced. 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. 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 (Avh) genes. We were able to clone homologous Avh loci from the P. ramorum sister-taxa P. lateralis and P. hibernalis. Availability of the P. ramorum genome sequence has also resulted in several practical applications including identifying which genes are differentially expressed during different pathogen life-stages and during plant infection. The genome has been mined for molecular loci that can be used for pathogen identification and genotyping. Both the P. ramorum and P. sojae genomes have been used to select sequence loci for the construction of a phylogeny of the genus Phytophthora The P. ramorum 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. Availability of the P. ramorum and P. sojae genome sequences has already provided advances and a new understanding of Phytophthora biology. Many promising new discoveries are sure to follow.

Keywords: Phytophthora ramorum, comparative genomics, genome

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Citation

Grünwald, Niklaus J.   2008.  What can availability of the Phytophthora ramorum genome do for us?.   In: Frankel, Susan J.; Kliejunas, John T.; Palmieri, Katharine M., tech. coords. 2008. Proceedings of the sudden oak death third science symposium. Gen. Tech. Rep. PSW-GTR-214. Albany, CA: U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station. pp. 233-238.