I am a third year graduate student in the laboratory of Dr. Matthew Sullivan in the department of Ecology and Evolutionary Biology at the University of Arizona. I study the genome contents of natural communities of microbial viruses found in the world’s oceans. Although small and simple compared to living organisms, these viruses are numerous, and one can find millions of viruses in a single drop of ocean water. Viruses are also an important component of the ocean ecosystem, since they prey on the microbial life that forms the base of the ocean food web. As impactful as research on ocean viruses can be, my field is limited by the fact that most of them are currently difficult or impossible to grow in the laboratory, where they could be studied in depth. My dissertation work thus focuses on novel methods of studying viruses by looking at the genomic sequences of whole virus communities, or parts of these communities, through shotgun metagenomic read sequencing. Briefly, many viruses are collected from a few liters of seawater, their DNA is retrieved, broken into small pieces which can be “read” by a DNA sequencing instrument, and this fragmented information can then be pieced back together into the original viruses’ genomes using aseembly algorithms. Such virus genomes can tell us a lot about virus evolution and ecology, and maybe even a little about the microbes they infect.
Due to the novelty of metagenomic read sequencing, parts of these procedures were not yet rigorously evaluated. For my first graduate project I analyzed many methods of DNA sequencing to find the one best for ocean virus samples. This project resulted in a first author publication for me, with the manuscript currently under review at BMC Genomics. I am now moving on to several metagenomic sequencing projects to characterize virus evolutionary patterns: between natural ocean virus populations across the global oceans (a TARA Oceans Expedition collaboration), within viruses infecting a novel, highly abundant ocean bacterium called SAR11 (an Oregon State University collaboration), and across similar viruses infecting autotrophic ocean microbes Prochlorococcus and Synechococcus. Each of these projects relies on a thorough analysis of high-coverage sequencing data, and a large part of the analysis will be employing a phylogenetic species definition for microbial viruses. The analysis will include the generation of virus conserved gene trees, and also the evaluation of patterns of variation across these genes. Unfortunately, I realize that I am missing practical experience with large-scale phylogenetic analysis and application of population genetic methods, which is why I am very excited to apply for the Molecular Evolution Workshop. The training that I hope to acquire will be useful in key aspects of my dissertation research, and would also be helpful in smaller collaboration on other projects with members of my lab which study virus isolate genomes.