Progress 10/01/10 to 09/30/11
Outputs
Progress Report Objectives (from AD-416) 1. Generate assemblies from genomic sequence data for seven strains of Pseudomonas spp. 2. Oversee the automated annotation of the genomes that will be done at JCVI. 3. Using an array of bioinformatic tools, compare the genomes of the seven strains including the identification of the lineage-specific regions of each strain. Approach (from AD-416) Oversee the generation of assemblies and automatic annotation of seven genomes. Oversee the automated annotation of the genomes. Using an array of bioinformatic tools, compare the genomes of the seven strains including the identification of the lineage-specific regions of each strain. Biological control represents a promising approach for sustainable disease management in the future, and Pseudomonas is an important genus of biological control agents. The goal of this project is to improve knowledge of biological control by analyzing the genomic sequences of strains of Pseudomonas spp. that suppress plant disease. During this project period, collaborators at Macquarie University provided in depth analysis of genomic sequence data obtained earlier. The seven genomes were compared with all available genomes of Pseudomonas species using a multiway BLASTP analysis, and putative orthologs were identified with an E-value cutoff of 10-30. A core genome of 2831 proteins was identified for the Pseudomonas fluorescens intrageneric cluster. This core genome represents only 46% to 53% of the proteome of each strain, indicating a large degree of genomic diversity in this group of bacteria. Genes conserved among all of the genomes encode proteins contributing mainly to fundamental housekeeping functions whereas genes present in only one to a few strains may confer traits underpinning the diverse ecology of this bacterial group. The seven newly-sequenced Pseudomonas genomes were examined for the presence of repetitive extragenic palindromic (REP) elements. Two distinct REP-like elements occurring at least 250 times were observed within non-coding regions of the seven genomes. One of the two elements appears to be conserved across all biocontrol strains. The secondary REP elements were present in one to four strains. The functions of REP regions are unknown, but it is possible that the two shared REP elements have similar functions in all strains whereas the strain- specific REP elements have different functions. The successful colonization and persistence of plant biocontrol bacteria on plant surfaces relies on their ability to acquire sufficient nutrients found in these environments. The seven strains were evaluated for their utilization (catabolism) of a panel of diverse carbon and nitrogen substrates, and the catabolic profiles were related to sequence data. The information obtained from this project is providing new insight into the genes contributing to plant disease suppression or environmental fitness of bacteria beneficial to plants. Methods of project monitoring included meetings, e-mail, and phone calls.
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Progress 10/01/09 to 09/30/10
Outputs
Progress Report Objectives (from AD-416) 1. Generate assemblies from genomic sequence data for seven strains of Pseudomonas spp. 2. Oversee the automated annotation of the genomes that will be done at JCVI. 3. Using an array of bioinformatic tools, compare the genomes of the seven strains including the identification of the lineage-specific regions of each strain. Approach (from AD-416) Oversee the generation of assemblies and automatic annotation of seven genomes. Oversee the automated annotation of the genomes. Using an array of bioinformatic tools, compare the genomes of the seven strains including the identification of the lineage-specific regions of each strain. Documents Grant with Macquarie University. We have continued comparative genomic analyses of seven strains of Pseudomonas spp. that function in biological control of plant disease. The putative origins of replication have been identified in each genome and the genomes have been re-oriented with respect to the origin. Phylogenetic analyses of concatened, conserved, orthologous genes in the genomes has clarified the evolutionary history of the biocontrol pseudomonads and allowed us to identify three distinct clades within this group. Lineage-specific regions of the genomes were evaluated bioinformatically for the presence of genes that may contribute to biological control or environmental fitness of Pseudomonas spp., and we have identified secondary metabolite biosynthesis gene clusters specific to either particular strains or to one of the three clades. Genomes of the seven Pseudomonas spp. were analyzed for the presence of repeated sequences. Methods of ADODR monitoring included meetings, teleconferences, phone calls, e-mail and site visits.
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Progress 10/01/08 to 09/30/09
Outputs
Progress Report Objectives (from AD-416) 1. Generate assemblies from genomic sequence data for seven strains of Pseudomonas spp. 2. Oversee the automated annotation of the genomes that will be done at JCVI. 3. Using an array of bioinformatic tools, compare the genomes of the seven strains including the identification of the lineage-specific regions of each strain. Approach (from AD-416) Oversee the generation of assemblies and automatic annotation of seven genomes. Oversee the automated annotation of the genomes. Using an array of bioinformatic tools, compare the genomes of the seven strains including the identification of the lineage-specific regions of each strain. Documents Grant with Macquarie University. Significant Activities that Support Special Target Populations Comparative genomic analyses is underway on the draft genomic sequences of six well-characterized biocontrol strains of Pseudomonas spp. We have performed multi-way ortholog comparisons to identify conserved genes between strains and to identify novel genomic islands unique to each strain. The six strains share ca. 3100 genes that represent a core genome, and each strain has unique genes that are not found in the other genomes. The number of unique genes varies from 477 (P. chloraphis 30-84) to 893 (P. fluorescens Q8r1). We have also undertaken genome synteny/conservation analyses using MAUVE. Genes conserved among the biocontrol strains as well as those unique to each strain are the subject of current analysis to determine their potential roles in biological control or the plant-associated life style of these bacteria. The synteny analysis was also used to derive a strategy for closing some of the gaps in the draft genomic sequences, and this strategy has been employed successfully by collaborators on the project in other institutions. Methods of ADODR monitoring included meetings, e-mail and other written correspondence.
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Progress 10/01/07 to 09/30/08
Outputs
Progress Report Objectives (from AD-416) 1. Generate assemblies from genomic sequence data for seven strains of Pseudomonas spp. 2. Oversee the automated annotation of the genomes that will be done at JCVI. 3. Using an array of bioinformatic tools, compare the genomes of the seven strains including the identification of the lineage-specific regions of each strain. Approach (from AD-416) Oversee the generation of assemblies and automatic annotation of seven genomes. Oversee the automated annotation of the genomes. Using an array of bioinformatic tools, compare the genomes of the seven strains including the identification of the lineage-specific regions of each strain. Documents Grant with Macquarie University. Significant Activities that Support Special Target Populations Bioinformatic analysis of the genomic sequence data obtained by JVCI has begun March 1, 2008. There is no progress to report. Methods of ADODR monitoring include meetings, e-mail, and phone calls.
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