Proposal Title: Collaborative Research: PHANTOME: PHage ANnotation TOols and MEthods Institution: San Diego State University Foundation Abstract Date: 03/09/09 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. NATIONAL SCIENCE FOUNDATION Proposal Abstract Proposal:0850356 PI Name:Edwards, Robert Printed from eJacket: 03/10/09 Page 1 of 1
Our lab's contribution to the Phantome project was to curate RAST subsystems for phages with particular focus on the most abundant ocean viral types (T4- and T7-like phages), and protein clusters derived from the Pacific Ocean Virome dataset. A total of 456K protein clusters were annotated and made publicly available at the CAMERA metagenomics database, as well as the RAST subsystem annotation server. This doubles all known viral sequence space. These resources will be invaluable for organizing and analyzing viral genomes and metagenomes, particularly those derived from ocean ecosystems. Biological findings resulting from these annotation efforts are published in the following peer reviewed papers: 1. Hurwitz, B.H. & Sullivan, M.B. The Pacific Ocean Virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS One 8, e57355 (2013). 2. Ignacio-Espinoza, J.C. & Sullivan, M.B. Phylogenomics of T4 cyanophages: Lateral gene transfer in the "core" and origins of host genes Environ Microbiol 14, 2113-2126 (2012). 3. Labrie, S.J. et al. Genomes of marine cyanopodoviruses reveal multiple origins of diversity. Environmental Microbiology DOI: 10.1111/1462-2920.12053 (2013). 4. Sullivan, M.B. et al. Genomic analysis of oceanic cyanobacterial myoviruses compared to T4-like myoviruses from diverse hosts and environments. Environ Microbiol 12, 3035-3056 (2010).
