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.

Genome-Wide EST Data Mining Approaches to Resolving Incongruence of Molecular Phylogenies

“…100% support for the congruent tree from the concatenated alignments of 144 single genes regardless of the phylogenetic methods, even the simplest method such as NJAD, demonstrated power of large datasets by means of the genome-wide data mining approach in resolving the incongruence. Multiple-gene approaches such as three combined genes of angiosperms [19], four combined proteins of eukaryotes [16], six and nine genes of flowering plants [27], 23 proteins of bacteria, archea and eucarya [28], 63 genes of baculovirus [7] and 106 concatenated genes of yeasts [17] strengthened supports and improved the consistence of phylogenies. Those previous results were consistent with the result in this study.…”

“…Kluge believed that phylogenetic analysis should always be performed using all the evidences [14], but Miyamoto and Fitch argued that partitions (including genes) should not be combined [15]. Concatenated alignments of a couple of genes improved supports [3][4][5][6][7][8][9][10][11][12][13][14][15][16]. Concatenating alignments into one from genome-scale 106 genes based on 7 yeast genomes [17] for phylogenetic analysis proclaimed ending incongruence [18].…”

Hyphantria cunea Nucleopolyhedrovirus, a Novel Baculovirus Isolated from Fall Webworm in Korea

“…Nucleopolyhedroviruses also can be divided into two groups, group I and II, by phylogenetic analysis of several genes including polyhedrin (Zanotto et al, 1993;Herniou et al, 2001). The group I and II NPVs have divergent multiplication strategies on the entry mechanism of budded virus (BV) in haemocoel.…”

Genomic and host range studies of Maruca vitrata nucleopolyhedrovirus

“…The family Baculoviridae is subdivided into two genera, Nucleopolyhedrovirus (NPV) and Granulovirus (GV). Based on the polyhedrin (polh) gene, NPVs are further subdivided into group I and group II (Bulach et al, 1999;Herniou et al, 2001Herniou et al, , 2003. Recent evidence shown from the comparison of 29 baculovirus genomes indicates that baculovirus phylogeny is aligned with the classification of the hosts more closely than with morphological traits (Afonso et al, 2001;Garcia-Maruniak et al, 2004;Lauzon et al, 2004;Jehle et al, 2006).…”