Genomics Based Discovery of Novel Traits in Beneficial Plant-associated Pseudomonas Species
Horticultural Crops Research
2011 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 J.Craig Venter Institute.
Biological control represents a promising approach for sustainable disease management in the future, and Pseudomonas is an important genus of bacterial biological control agents. The goal of this project is to sequence the genomes of strains of Pseudomonas spp. that suppress plant disease, and provide sequence data to the scientific community to enhance knowledge of biological control. In previous years, J. Craig Venter Institute (JCVI) sequenced the genomes of seven well-characterized biological control strains of Pseudomonas spp. During this project period, JCVI continued to provide ARS with access to the sequence data and software needed for ARS scientists to annotate the genomes. JCVI also improved the sequence data by closing gaps, correcting sequencing errors, and rotating the chromosomal and plasmid sequences to correctly reflect the origin of replication of these molecules. JCVI prepared some of the sequence files for submission to the National Center for Biotechnology Information data bases, which will make the information available to the scientific community. They deposited to NCBI an updated sequence file for the genome of P. fluorescens Pf-5, which was improved substantially since it was first deposited in 2005. In summary, this project is providing the fundamental data needed for the ARS project on comparative genomics of biocontrol strains of Pseudomonas spp., which 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. Two workshops were conducted by the ARS scientist and collaborators.