Esteban and Hutchinson BMC Genomics 2011, 12:261 http://www.biomedcentral.com/1471-2164/12/261 R E S E A R C H A R T I C L E Open Access Genes in the terminal regions of orthopoxvirus genomes experience adaptive molecular evolution David J Esteban* and Anne P Hutchinson Abstract Background: Orthopoxviruses are dsDNA viruses with large genomes, some encoding over 200 genes. Genes essential for viral replication are located in the center of the linear genome and genes encoding host response modifiers and other host interacting proteins are located in the terminal regions. The central portion of the genome is highly conserved, both in gene content and sequence, while the terminal regions are more diverse. In this study, we investigated the role of adaptive molecular evolution in poxvirus genes and the selective pressures that act on the different regions of the genome. The relative fixation rates of synonymous and non-synonymous mutations (the dN/dS ratio) are an indicator of the mechanism of evolution of sequences, and can be used to identify purifying, neutral, or diversifying selection acting on a gene. Like highly conserved residues, amino acids under diversifying selection may be functionally important. Many genes experiencing diversifying selection are involved in host-pathogen interactions, such as antigen-antibody interactions, or the “host-pathogen arms race.” Results: We analyzed 175 gene families from orthopoxviruses for evidence of diversifying selection. 79 genes were identified as experiencing diversifying selection, 25 with high confidence. Many of these genes are located in the terminal regions of the genome and function to modify the host response to infection or are virion-associated, indicating a greater role for diversifying selection in host-interacting genes. Of the 79 genes, 20 are of unknown function, and implicating diversifying selection as an important mechanism in their evolution may help characterize their function or identify important functional residues. Conclusions: We conclude that diversifying selection is an important mechanism of orthopoxvirus evolution. Diversifying selection in poxviruses may be the result of interaction with host defense mechanisms. Background Poxviruses are a family of double stranded DNA viruses that infect diverse host species. The genus Orthopox- virus includes Variola (the causative agent of smallpox), Vaccinia (the smallpox vaccine), Monkeypox, an emer- ging human pathogen, and Cowpox. Poxviruses are among the largest and most complex of all animal viruses, some expressing over 200 genes [1]. A large fraction of the coding capacity of the genome is for processes essential for viral replication, such as vir- ion assembly, transcription and replication. Unlike other DNA viruses, poxviruses replicate in the cytoplasm and therefore encode all genes necessary for DNA * Correspondence: daesteban@vassar.edu Biology Department, Vassar College, 124 Raymond Ave, Poughkeepsie, NY, 12604, USA replication and transcription. These essential genes are highly conserved throughout the poxvirus family and in orthopoxviruses these core genes form a continuous block in the center of the linear genome [2,3]. Flanking the central region, the terminal regions of orthopoxvirus genomes show divergence among differ- ent genera, among species within a genus, and even among strains of the same species [4]. Many of these genes are non-essential for virus replication in cell cul- ture but are virulence factors that mediate interactions with the host cell or immune system in their natural host. These include immune evasion genes that inhibit cytokines [5], inhibit the interferon response [6], or block apoptosis [7]. Many of these are host species spe- cific, indicating adaptation to the specific host response to infection. © 2011 Esteban and Hutchinson; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.