Progress 01/01/07 to 12/31/11
Outputs
Progress Report Objectives (from AD-416): To use genomic sequence data from the mitochondrial DNA for systematic development of genus and species specific molecular markers for the genus Phytophthora. Approach (from AD-416): Purified mitochondrial DNA from a phylogenetically diverse range of species will be sequenced and the data used to develop species specific molecular markers. Genomes for a related genus Pythium also will be sequenced to allow for the development of genus specific markers. All markers will be tested against a broad range of species in both genera. The data will be made available to the public via a web-based data base. The agreement was established in support of Objective 2 of the in house project, the goal being to develop molecular diagnostic tools for the identification of emerging diseases of vegetables and strawberries, and use these tools in the development of management strategies as alternatives to methyl bromide. Three different gene order differences were observed between Phytophthora and Pythium as well as between Phytophthora and plants based on comparisons of mitochondrial. The marker system was designed for TaqMan Real Time PCR with a genus-specific probe that anneals to a highly conserved coding region of the amplicon and species-specific probes designed against an adjacent spacer region. This region has been sequenced in 500+ isolates that represent the geographic range of all Phytophthora spp. The polymorphisms observed in this region should enable the of design species-specific probes for over 80 Phytophthora spp. (Species specific probes have been validated for 14 species using 400+ DNAs supplied by a collaborator). These markers are currently being validated using environmental samples. Techniques for rapidly determining the mitochondrial haplotypes of Phytophthora ramorum (the cause of sudden oak death) were perfected (melt curve analysis of PCR amplified mitochondrial DNA). Mitochondrial haplotype analysis on 62 isolates of Phytophthora cinnamomi was completed with 45 haplotypes identified.
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Progress 10/01/10 to 09/30/11
Outputs
Progress Report Objectives (from AD-416) To use genomic sequence data from the mitochondrial DNA for systematic development of genus and species specific molecular markers for the genus Phytophthora. Approach (from AD-416) Purified mitochondrial DNA from a phylogenetically diverse range of species will be sequenced and the data used to develop species specific molecular markers. Genomes for a related genus Pythium also will be sequenced to allow for the development of genus specific markers. All markers will be tested against a broad range of species in both genera. The data will be made available to the public via a web-based data base. The objective of the project is to use comparative genomics of the mitochondrial genome of Phytophthora spp, to address questions of evolutionary relationship in the genus and employ a systematic approach for development of molecular markers capable f identifying individual species. Mitochondrial genomes have been sequenced for 18 Phytophthora species. Based on comparison with the mitochondrial genomes of 14 Pythium spp. three different gene order differences were observed between these two genera as well as between Phytophthora and plants. The marker system was designed for TaqMan real time polymerase chain reaction with a genus specific probe that anneals to a highly conserved coding region of the amplicon and species-specific probes designed against an adjacent spacer region. This region has been sequenced for over 500 isolates representing a geographic range of all Phytophthora spp. and with the polymorphisms observed in this region it should be possible to design species-specific probes for over 80 Phytophthora spp. (species specific probes have been developed for 14 species). These markers are currently being validated using 400+ DNAs supplied by a collaborator as well as with field samples. Techniques for rapidly determining the mitochondrial haplotypes of Phytophthora ramorum (the cause of sudden oak death) were perfected (melt curve analysis of PCR amplified mitochondrial DNA). Mitochondrial haplotype analysis on 62 isolates of Phytophthora cinnamomi was completed with 45 haplotypes identified. Communication on the project status is done with the granting agency by e-mail and submission of written yearly progress reports.
Impacts
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Progress 10/01/09 to 09/30/10
Outputs
Progress Report Objectives (from AD-416) To use genomic sequence data from the mitochondrial DNA for systematic development of genus and species specific molecular markers for the genus Phytophthora. Approach (from AD-416) Purified mitochondrial DNA from a phylogenetically diverse range of species will be sequenced and the data used to develop species specific molecular markers. Genomes for a related genus Pythium also will be sequenced to allow for the development of genus specific markers. All markers will be tested against a broad range of species in both genera. The data will be made available to the public via a web-based data base. Documents Reimbursable with NRI-CGP. Log 31655. Formerly 5305-22000-009- 12R (12/07). This report serves to document research conducted under a reimbursable agreement between ARS and the USDA-CSREES-NRI grant program that has a collaborator at the Joint Genome Institute as a co-PI. Addition details of research can be found in the report for the parent CRIS 5305 22000 012 00D. The objective of the project is to use comparative genomics of the mitochondrial genome of Phytophthora spp. to address questions of evolutionary relationship in the genus and employ a systematic approach for development of molecular markers capble of identifying individual species. Mitochondrial genomes have been sequenced for 18 Phytophthora species. Based on comparison with the mitochondrial genomes of 14 Pythium spp. three different gene order differences were observed between these two genera as well as between Phytophthora and plants. Based on preliminary sequence data from 90 species of Phytophthora one region was selected to be the focus for marker development. The marker system was designed for TaqMan real time PCR with a genus specific probe designed to anneal to a highly conserved coding region of the amplicon and species- specific probes designed against the spacer region between the two flanking genes. This region has been sequenced for 525 isolates representing a geographic range of all Phytophthora spp. and with the polymorphisms observed in this region it should be possible to design species-specific probes for over 80 Phytophthora spp. (species specific probes have been developed for 13 species). These markers are currently being validated using 400+ DNAs supplied by a collaborator as well as with field samples. Techniques for rapidly determining the mitochondrial haplotypes of Phytophthora ramorum (the cause of sudden oak death) were perfected (melt curve analysis of PCR amplified mitochondrial DNA). Mitochondrial haplotype analysis on 62 isolates of Phytophthora cinnamomi was completed with 45 haplotypes identified. Communication on the project status is done with the granting agency by e-mail and submission of written yearly progress reports.
Impacts
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Progress 10/01/08 to 09/30/09
Outputs
Progress Report Objectives (from AD-416) To use genomic sequence data from the mitochondrial DNA for systematic development of genus and species specific molecular markers for the genus Phytophthora. Approach (from AD-416) Purified mitochondrial DNA from a phylogenetically diverse range of species will be sequenced and the data used to develop species specific molecular markers. Genomes for a related genus Pythium also will be sequenced to allow for the development of genus specific markers. All markers will be tested against a broad range of species in both genera. The data will be made available to the public via a web-based data base. Documents Reimbursable with NRI-CGP. Log 31655. Formerly 5305-22000-009- 12R (12/07). Significant Activities that Support Special Target Populations The objective of the project is to use comparative genomics of the mitochondrial genome of Phytophthora spp. to address questions of evolutionary relationship in the genus and employ a systematic approach for development of molecular markers capble f identifying individual species. Mitochondrial genomes have been sequenced for 18 Phytophthora species. Based on comparison with the mitochondrial genomes of 14 Pythium spp. three different gene order differences were observed between these two genera as well as between Phytophthora and plants. These regions were sequenced for 90 species of Phytophthora and primers developed for a real-time PCR Phytophthora genus specific marker. Techniques for rapidly determining the mitochondrial haplotypes of Phytophthora ramorum (the cause of sudden oak death) were perfected (melt curve analysis of PCR amplified mitochondrial DDNA). The specificity of the primers are currently under evaluation. Communication on the project status is done with the granting agency by e-mail and submission of written yearly progress reports.
Impacts
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Progress 10/01/06 to 09/30/07
Outputs
Progress Report Objectives (from AD-416) To use genomic sequence data from the mitochondrial DNA for systematic development of genus and species specific molecular markers for the genus Phytophthora. Approach (from AD-416) Purified mitochondrial DNA from a phylogenetically diverse range of species will be sequenced and the data used to develop species specific molecular markers. Genomes for a related genus Pythium also will be sequenced to allow for the development of genus specific markers. All markers will be tested against a broad range of species in both genera. The data will be made available to the public via a web-based data base. Documents Reimbursable with NRI-CGP. Log 31655 Significant Activities that Support Special Target Populations This report serves to document research conducted under a reimbursable agreement between ARS and the USDA-CSREES-NRI grant program that has a collaborator at the Joint Genome Institute as a co-PI. Additional details of research can be found in the report for the parent CRIS 5305 22000 009 00D. The objective of the project is to use comparative genomics of the mitochondrial genome of Phytophthora spp. to address phylogenetic questions in the genus and employ a systematic approach for development of species-specific markers. This is the first year of the three-year project. Mitochondrial DN is in the process of being purified form an additional 15 isolates of Phytophthora and will be sent out to the JGI for sequencing in the near future. Based on the analysis of mitochondrial genomes of 12 Phytophthora and 14 Pythium spp. gene order differences were observed between these tow genera as well as between Phytophthora and plants. This region has been sequenced for 70 species of Phytophthora and primers developed for a real-time PCR Phytophthora genus specific marker. The specificity of the primers is currently under evaluation. Communication on the project status is done with the granting agency by e- mail and submission of written yearly progress reports.
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