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Sequences reveal benign origin of deadly plant pathogens
September 01, 2006An international team of researchers has published the draft genome sequences of two deadly plant pathogens, Phytophthora ramorum and Phytophthora sojae. Phytophthora sojae causes severe damage in soybean crops and results in $1-2 million in annual losses for commercial farmers in the United States. Phytophthora ramorum, which causes sudden oak death, has attacked and killed tens of thousands of oak trees in California and Oregon. The sequences of both genomes, which are described in the September 1 issue of Science, reveal a recent, large expansion and diversification of many deadly genes involved in infection of the plant hosts of Phytophthora.
The sequence information shows how Phytophthora most likely evolved from a benign photosynthetic ancestor into a sophisticated, plant-killing machine. Phytophthora belongs to the kingdom Stramenopila, which also includes golden-brown algae, diatoms and kelp. Around 1300 million years ago, some or perhaps all stramenopiles acquired the ability to harness light for their energy needs by assimilating photosynthetically competent organisms. Today however, some stramenopiles, including Phytophthora, are non-photosynthetic. Did the kingdom arise from a photosynthetic or non-photosynthetic organism? A close look at the new sequence data shows as many as 800 genes with a potential photosynthetic origin, strongly supporting the hypothesis that the stramenopile ancestor was a photosynthetic organism, and that Phytophthora lost this capability as it became a parasite.
The genome sequences reveal that P. sojae and P. ramorum have a large number of genes compared to counterparts such as pathogenic fungi; 19 027 likely genes were identified in P. sojae and 15 743 in P. ramorum. The sequences also clearly indicate a recently acquired, large armory of proteins that enable the pathogens to attack their plant hosts.
Professor Brett Tyler of the Virginia Bioinformatics Institute, one of the leaders of the project, remarked: "The extraordinarily large and plastic array of pathogenicity genes that has been unveiled by the genome sequences provides us with a major insight into the basis for the success of this group of pathogens." A comparison of the genomes of the two Phytophthora species shows a rapid expansion and diversification of many protein families linked to plant infection, including toxins, protein inhibitors and enzymes that can break down cell walls. In particular, a group of genes encoding a large family of secreted proteins (the secretome) is evolving much more rapidly than other protein-coding genes. Secreted proteins are intimately involved in the mechanism of pathogenesis.
Professor Jeffrey Boore, a co-leader of the project from the US Department of Energy (DOE) Joint Genome Institute, remarked: "This has been a ground-breaking, large-scale, collaborative project. As a resource for the entire scientific community, it is already having an immediate impact on plant pathogen research. To take one example, the P. ramorum sequence has over 13 000 single nucleotide polymorphisms, which has already led to the development of genetic markers for population studies and for tracking the movement of different strains of P. ramorum. Further, this was the first case where researchers were able to infer gene function from actual evolutionary analyses based on the pipeline we have developed at http://PhIGs.org."
Professor Tyler added: "The sequences are a fundamental resource with wide-ranging applications for the Phytophthora community. We will be pursuing our investigations of the secreted proteins linked to damage of the plant host in the hope of developing much needed countermeasures against these deadly pathogens."
Virginia Tech
Professor Brett Tyler of the Virginia Bioinformatics Institute, one of the leaders of the project, remarked: "The extraordinarily large and plastic array of pathogenicity genes that has been unveiled by the genome sequences provides us with a major insight into the basis for the success of this group of pathogens." A comparison of the genomes of the two Phytophthora species shows a rapid expansion and diversification of many protein families linked to plant infection, including toxins, protein inhibitors and enzymes that can break down cell walls. In particular, a group of genes encoding a large family of secreted proteins (the secretome) is evolving much more rapidly than other protein-coding genes. Secreted proteins are intimately involved in the mechanism of pathogenesis.
Professor Jeffrey Boore, a co-leader of the project from the US Department of Energy (DOE) Joint Genome Institute, remarked: "This has been a ground-breaking, large-scale, collaborative project. As a resource for the entire scientific community, it is already having an immediate impact on plant pathogen research. To take one example, the P. ramorum sequence has over 13 000 single nucleotide polymorphisms, which has already led to the development of genetic markers for population studies and for tracking the movement of different strains of P. ramorum. Further, this was the first case where researchers were able to infer gene function from actual evolutionary analyses based on the pipeline we have developed at http://PhIGs.org."
Professor Tyler added: "The sequences are a fundamental resource with wide-ranging applications for the Phytophthora community. We will be pursuing our investigations of the secreted proteins linked to damage of the plant host in the hope of developing much needed countermeasures against these deadly pathogens."
Virginia Tech
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