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United States Department of Agriculture

Agricultural Research Service

Research Project: Genomics Based Discovery of Novel Traits in Beneficial Plant-associated Pseudomonas Species

Location: Horticultural Crops Research

2009 Annual Report

1a.Objectives (from AD-416)
1. Generate draft genomic sequences for seven plant-associated strains of Pseudomonas spp. that suppress plant disease. 2. Generate assemblies of the genomes. 3. Perform automatic annotation of the genomes. 4. Provide an instructor and materials for a workshop for 14 collaborators.

1b.Approach (from AD-416)
Prepare random genomic shotgun libraries and sequence both ends of randomly selected clones. Assemble genome from shotgun libraries and sequencing. For initial identification of protein coding sequences, the Glimmer algorithm will be used. All regions of a genome without Glimmer predictions will then be re-evaluated using BLASTP to search against a database of non-redundant proteins (nraa) maintained at JCVI. Documents Grant with J. Craig Venter Institute.

3.Progress Report

High quality draft sequences of six well-characterized biocontrol strains of Pseudomonas spp. have been completed. These six strains fall into three different species (P. fluorescens, P. chlororaphis, and P. synxantha), but they all reside within the “Pseudomonas fluorescens complex” of intrageneric cluster II of Pseudomonas spp. The genomes have been assembled and the assemblies are in 7 to 15 scaffolds, depending on the strain. The genomes vary in size from 6.02 Megabases with 5547 predicted ORFs (strain A506) to 6.69 Megabases with 6437 predicted ORFs (strain O-6). The assembled genomes have undergone an automated annotation. JCVI hosted a bioinformatics course in March of 2009 in which two collaborators on this project participated. The collaborators learned how to use the Manatee annotation program, and returned to their labs with a working knowledge of how to annotate the Pseudomonas genomes. To facilitate annotation, JCVI clustered the six new genomes with the fully sequenced genome of Pf-5, allowing genes from all seven genomes to be annotated as a group. This clustering has been a very effective approach, advancing the annotation of all genomes. JCVI also did an indepth phylogenetic analysis of each gene in the six new genomes, and made these phylogenetic trees available to the team of collaborators on the project. JCVI provided web access for all collaborators on the project to the genomic sequences.

Methods of ADODR monitoring included meetings, e-mail and other written correspondence.

Last Modified: 4/19/2014
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