Collaborative Research: PHANTOME: PHage ANnotation TOols and MEthods

San Diego State University Foundation, San Diego CA

Investigators

Abstract

Viruses are the most abundant biological entities on the planet. Since the most abundant living organisms on Earth are bacteria, the majority of these viruses are phages, the viruses which infect bacteria. Through their diverse lifestyles and gene products, phages play important roles in horizontal gene exchange, in structuring natural microbial communities, and in global biogeochemical cycles. Phages carry genes for some of the deadliest toxins known and can also carry genes which confer adaptive advantages to the hosts they infect. Furthermore, phage genes and the proteins they encode are the outcome of evolution over eons, the products of which we would be able to exploit if only we could decode the information in the phage DNA sequences. The number of available phage genome sequences is increasing rapidly; on the other hand, they represent the largest global reservoir of uncharacterized genetic material. Bioinformatic tools necessary for interpreting this data has lagged behind the growth in genome sequences. Grants to develop a platform and toolbox of computational tools for phage genome analysis have been awarded to support collaborative research in the laboratories of Drs. Robert Edwards, Department of Computer Sciences, San Diego State University, Mya Breitbart, College of Marine Sciences, University of South Florida, Jeffrey Elhai, Biology Department, Virginia Commonwealth University and Matthew Sullivan, Department of Ecology and Evolutionary Biology, University of Arizona. Dr. Elhai is an Associate Professor, the other three investigators are Assistant Professors. This collaborative project is creating new computational tools to establish a consistent nomenclature for phage genomes, to annotate phage sequences, both from completely sequenced phage genomes and from environmental phage metagenome sequences. Most importantly, this project will engage a wide spectrum of researchers, regardless of their computational background, to access the wealth of information contained in phage genomes through familiar graphical interfaces. These collaborators have developed an extensive and far-reaching education plan that targets high school students, undergraduate students and graduate students. The students trained in the use of the tools will rotate into trainer roles via user forums and workshops. The postdocs will be working across all the labs and thereby gain an unparalleled panoramic view of phage biology.