Use of whole genome sequence data to infer baculovirus phylogeny

Abstract

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.

FIG. 1

Gene sequence phylogenies. (a) Majority rule consensus tree of the most parsimonious trees obtained for each of the 63 genes shared by all nine baculoviruses. The numbers indicate the percentages of individual gene trees supporting each branch. (b) Most parsimonious tree based on the combined sequences of the 63 shared genes. Numbers indicate the percentages of bootstrap support from 1,000 replicates. Trees are rooted using the GVs as a sister group to the NPVs.

FIG. 2

Gene order phylogenies. (a) Neighbor-joining tree based on relative breakpoint distances. (b) Most parsimonious tree based on the neighboring gene pair analysis. Numbers indicate the percentages of bootstrap support from 1,000 replicates. Trees are rooted using the GVs as a sister group to the NPVs.

FIG. 3

Gene content phylogeny. Most parsimonious tree based on the gene content data set. Percentages of bootstrap support (1,000 replicates) greater than 50% are shown. The tree is rooted using the GVs as a sister group to the NPVs.

FIG. 4

odv-e66 (a) and polyhedrin (b) gene phylogenies. The single most parsimonious tree is shown in each case. Percentages of bootstrap support (1,000 replicates) greater than 50% are shown. Trees are rooted using the GVs as a sister group to the NPVs.

FIG. 5

Gene content data mapped onto the most parsimonious tree based on the combined sequences of the 63 common genes. Shown are gene content changes predicted to have taken place during baculovirus evolution. Gene acquisitions and losses are represented by solid and open symbols, respectively. Where the state of a gene is predicted to have changed only once, a rectangle is used, whereas triangles are used to denote genes whose state has changed multiple times. An upward-pointing triangle is used to illustrate where the additional change of state occurs further up in the same lineage. For example, ac18 is acquired at the base of the NPV lineage but is subsequently lost from the HaSNPV lineage. Downward-pointing triangles illustrate where the character state of a gene changes independently in different parts of the lineage. For example, DNA ligase, helicase 2, and p13 are represented by downward-pointing triangles at the base of the GV lineage because all three genes are also independently acquired by some NPVs. Only gene content changes that can be unambiguously assigned to a particular branch are shown, with the exception of gene content changes leading to the separation of NPVs and GVs (see the text for details). The tree is rooted using the GVs as a sister group to the NPVs.

FIG. A1

Most-parsimonious tree topologies obtained for the individual phylogenetic analyses of the 63 shared genes and for the combined gene alignment, gene order, and gene content data sets. Table A1 shows which data set(s) gave rise to each tree.