Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Phages Of Burkholderia: A Student-Based Genomics Approach

Elizabeth J Summer¹ , Linet Mera¹ , Stephen Robinson¹ , Alyssa Rosenbloom¹ , Carlos F. Gonzalez² , Ryland Young¹

¹  Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128 USA

²  Department of Plant Pathology and Microbiology, Texas A&M University, College Station. TX 77843 USA

We have been utilizing phage as a vehicle to introduce undergraduate students to a shotgun approach to whole genome sequencing. To date, over 70 undergraduates have been involved in sequencing 16 phages (BcepMu, Bcep1, Bcep781, Bcep43, BcepF1, BcepB1A, BcepNazgul, Bcep176, Bcep22, BcepC6B, Bglu421, Era103, BcepGomr, BcepEtu, BcepFife, BcepBrny). These Bcep phages infect members of the Burkholderia cepacia complex (BCC) which includes opportunistic human pathogens, soil saprophytes, and phytopathogens. Our phage collection includes many virulent environmental isolates, primarily from high organic content soils known to harbor BCC. These are all dsDNA tailed phage with genomes of less then 100 kb. Students participate in all levels of the program, from phage isolation to library preparation, shotgun and finishing the genomic sequence and annotation and submission of completed genomes to GenBank. These phages underscore the complexity of the total phage population. For example, phages, Bcep176 and Bglu421, are representatives of the two lysogen types present in several sequenced Burkholderiaceae. In contrast, the closest relatives of BcepMu are lysogens of Salmonella and Photorhabdus. Bcep781, Bcep43, and Bcep1 are over 90% identical at a nucleotide level and exhibit a rate of synonymous substitutions indicative of neutral genetic drift. A goal of this project is to generate experimental data to support the bioinformatic and genomic analysis. For example, a surprising number of our phages possess SAR endolysins or novel endolysins with only limited homology to known endolysins. The identity of these endolysins has been confirmed using a biochemical approach. Grant # NSF0135653