Detection and analysis of horizontal gene transfer in herpesvirus

Horizontal gene transfers, where a significant proportion of the coding DNA is contributed by external sources, might give rise to extremely dynamic genomes, which brings impact on the ecological and pathogenic characters of the recipient organisms. Therefore it is important to computationally discriminate between horizontal transferred genes and normal genes. In this paper, we introduce a novel method for identifying horizontal transferred genes. This method, which relies on a gene's nucleotide composition and hence obviates the need for knowledge of codon boundaries, is able to detect the horizontal transferred genes with an accuracy of higher than 90% within a reasonable length of time by using just a common PC. With this method, 141 putative transferred genes in mammalian herpesvirus were identified. Among them, 16 genes had been predicted or reported to have cellular homologues in previous papers, including those involved in immune systems and apoptosis such as GCR in EHV-2, BCL-2 (Bcelllymphoma/leukemia-2) homologue in MuHV-4, etc., and had been suggested being acquired from other organisms. Other 125 genes were identified for the first time. Twelve of the newly identified putative transferred genes had also been reported to participate in immune response, apoptosis, cell proliferation control or virulence determinant. Moreover, 42 of the 141 putative transferred genes were found to have non-virus homologues and so were convincingly revealed as transferred genes. Nine of the 42 transferred genes were phylogenetically analyzed, the origin and the relative origin time of which were discussed.