Microbial Genome Sequencing: Phages of Agronomic Bacteria: A Student Based Genomics Approach

Texas A&M Research Foundation, College Station TX

Investigators

Abstract

An NSF-funded program of undergraduate-based bacteriophage genomics has been developed. Bacterial viruses, or bacteriophages, are by far the most numerous biological entities on the planet and play a dominant role in the ecology of bacteria in all environments. Moreover, the virulence of bacterial pathogens for plants and animals, including humans, is often determined and transmitted by bacteriophages. Bacteriophage genomics is uniquely suited for introducing undergraduates to real research for several reasons. Bacteriophage genomes are small enough for an undergraduate team to achieve sufficient "shotgun" sequence coverage and preliminary annotation in a semester's laboratory effort. Moreover, the high-throughput necessary for microbial and eukaryotic genome projects is of less value in phage genomics. This is due in part to the necessity for careful manual annotation of the genomes, which are dense in relatively small genes that are frequently unrelated to any database entries. In this process, students achieve an in-depth immersion into important concepts from gene structure to viral biology. The specific scientific goal is to sequence 15 diverse, virulent bacteriophage genomes of the agronomically and clinically important group of soil bacteria, the Burkholderia cepacia complex (BCC). In addition to bioinformatics-based annotations, students will identify structural protein genes through mass spectrometry analysis of virions. Also, the structure of the linear dsDNA genomic termini will be determined. Students will perform experiments to determine host range, progeny burst size and lysis gene characterization. In addition to generating data of scientific importance, the undergraduates in the bacteriophage genomics program have consistently indicated that it is a unique and powerful way to inform and empower them as to whether science is a real career option. A web site describing the organizational structure of the course, the experimental protocols that are employed and the annotation of the sequenced bacteriophage will be established.