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Journal of Virology, September 2001, p. 8117-8126, Vol. 75, No. 17
0022-538X/01/$04.00+0   DOI: 10.1128/JVI.75.17.8117-8126.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.

Use of Whole Genome Sequence Data To Infer Baculovirus Phylogeny

Elisabeth A. Herniou,1,2 Teresa Luque,1 Xinwen Chen,3 Just M. Vlak,3 Doreen Winstanley,4 Jennifer S. Cory,2 and David R. O'Reilly1,*

Department of Biology, Imperial College, London SW7 2AZ,1 Ecology and Biocontrol Group, Centre for Ecology and Hydrology-Oxford, Oxford OX1 3SR,2 and Horticulture Research International, Wellesbourne,4 United Kingdom, and Laboratory of Virology, Wageningen University, Wageningen, The Netherlands3

Received 21 March 2001/Accepted 18 May 2001

Several phylogenetic methods based on whole genome sequence data were evaluated using data from nine complete baculovirus genomes. The utility of three independent character sets was assessed. The first data set comprised the sequences of the 63 genes common to these viruses. The second set of characters was based on gene order, and phylogenies were inferred using both breakpoint distance analysis and a novel method developed here, termed neighbor pair analysis. The third set recorded gene content by scoring gene presence or absence in each genome. All three data sets yielded phylogenies supporting the separation of the Nucleopolyhedrovirus (NPV) and Granulovirus (GV) genera, the division of the NPVs into groups I and II, and species relationships within group I NPVs. Generation of phylogenies based on the combined sequences of all 63 shared genes proved to be the most effective approach to resolving the relationships among the group II NPVs and the GVs. The history of gene acquisitions and losses that have accompanied baculovirus diversification was visualized by mapping the gene content data onto the phylogenetic tree. This analysis highlighted the fluid nature of baculovirus genomes, with evidence of frequent genome rearrangements and multiple gene content changes during their evolution. Of more than 416 genes identified in the genomes analyzed, only 63 are present in all nine genomes, and 200 genes are found only in a single genome. Despite this fluidity, the whole genome-based methods we describe are sufficiently powerful to recover the underlying phylogeny of the viruses.

* Corresponding author. Mailing address: Department of Biology, Imperial College of Science, Technology, and Medicine, Imperial College Rd., London SW7 2AZ, United Kingdom. Phone: 44 (0)20 75945376. Fax: 44 (0)20 75842056. E-mail: d.oreilly{at}ic.ac.uk.

Journal of Virology, September 2001, p. 8117-8126, Vol. 75, No. 17
0022-538X/01/$04.00+0   DOI: 10.1128/JVI.75.17.8117-8126.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.


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