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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
2008 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

Genomic libraries with a 6-8 Kb insert size were constructed for each strain, for use in shotgun sequencing. To date, approximately 1000 clones from each library have been sequenced for quality control purposes. Each library was found to meet quality control standards, and so the genomic sequencing of each has begun. In preparation for pyrosequencing, the genomic DNA of each strain was nebulized, subjected to emulsion PCR, and evaluated for quality control purposes. For each strain, the genomic DNA prepared for pyrosequencing was found to meet quality control standards, and pyrosequencing has been scheduled.

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


Last Modified: 12/28/2014
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