Sequencing and characterization of virus genomes

William H. Wilson and Declan Schroeder

Full Citation: Wilson, W. H., and D. Schroeder. 2010. Sequencing and characterization of virus genomes, p. 134-144. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual of Aquatic Viral Ecology. ASLO. [DOI 10.4319/mave.2010.978-0-9845591-0-7.134]

ABSTRACT: By unraveling the genetic code of viruses, genome sequencing offers a new era for aquatic virus ecology giving access to ecological function of viruses on an unprecedented scale. Although this chapter starts with the suggestion to that virus genome sequencing should be conducted professionally if financially feasible, we essentially try and guide the reader through some of the procedures that will direct a novice through a genome sequencing project. Arguably, the most important recommendation is to start with as high purity virus nucleic acid as possible. We use the adage, junk in equals junk out. Once sequence information is obtained, there is plenty of free, user-friendly software available to help build, annotate, and then compare sequence data. Acquiring metadata is another important aspect that is not often considered when embarking on a genome project. A new initiative by the Genomic Standards Consortium has introduced Minimum Information about a Genome Sequence (MIGS) that allows standardization of the way the data are collected to make it useful for downstream post-genomic analyses. Most viruses sequenced to date have produced surprises, and there is more to come from the other 1031 viruses still to be sequenced. This chapter focuses on sequencing purified virus isolates rather than virus metagenomes.