Genus specific evolution of codon usage and nucleotide compositional traits of poxviruses Sourav RoyChoudhury • Archana Pan • Debaprasad Mukherjee Received: 29 October 2010 / Accepted: 28 December 2010 / Published online: 11 January 2011 Ó Springer Science+Business Media, LLC 2011 Abstract Poxviruses are complex in their nucleotide compositional features of the coding regions. The codon usages in Poxviruses are in accordance with their compo- sitional bias. In the Poxviridae family, codon usage pat- terns and nucleotide compositional traits are widely divergent across species but some conservation was observed within a genus. Viruses from six Chordopox genera, i.e., Avipoxvirus, Capripoxvirus, Cervidpoxvirus, Orthopoxvirus, Suipoxvirus, Yatapoxvirus, and one Ento- mopox genus- Betaentomopoxvirus, and some unclassified Entomopoxvirus are significantly rich in AT composition. Four other Chordopox genera- Molluscipoxvirus, Ortho- poxvirus, Parapoxvirus, and some unclassified Chordo- poxvirus are dominated by the GC rich viruses. Poxviruses from these AT rich and GC rich genera preferred AT or GC ending codons owing to their respective nucleotide compositional bias. For example, viruses from AT rich Orthopoxvirus, or GC rich Parapoxvirus have evolved with mutually exclusive type codon preferences following their genus-specific nucleotide compositions. Additional factors like gene length and expression level also influenced their codon usage patterns to some extent in some Poxvirus genera. Evidences from correspondence analysis and cluster analysis on the extent of divergence in codon usage also support this genus specific evolution of Poxvirus codon usage. Analyzes suggest that most of the Poxviruses from different genera, have evolved in almost two different evolutionary trajectory in context of their nucleotide composition and codon usage. Keywords Codon usage bias Á Nucleotide composition Á Correspondence analysis Á Cluster analysis Á Poxvirus Á Evolution Abbreviations ORF Open reading frame ENC Effective number of codons RSCU Relative synonymous codon usage CAI Codon adaptation index COA Correspondence analysis Introduction Poxvirus infections can be traced back to the early history of human civilizations [1]. The severe most form of Poxvirus infection in human is smallpox (Variola virus). Though it has been eradicated as a disease in 1977 through world wide effort led by WHO (World Health Organization) [2], still Electronic supplementary material The online version of this article (doi:10.1007/s11262-010-0568-2) contains supplementary material, which is available to authorized users. S. RoyChoudhury Á D. Mukherjee (&) School of Information Technology, Bengal Engineering and Science University, Shibpur Howrah 711103, West Bengal, India e-mail: mdebaprasad@gmail.com S. RoyChoudhury e-mail: src_4u@yahoo.co.in A. Pan Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry 605014, India e-mail: archana@bicpu.edu.in D. Mukherjee Department of Information Technology, Dr. B.C. Roy Engineering College, Durgapur 713206, West Bengal, India Present Address: S. RoyChoudhury School of Medical Science and Technology, Indian Institute of Technology-Kharagpur, Kharagpur 721302, West Bengal, India 123 Virus Genes (2011) 42:189–199 DOI 10.1007/s11262-010-0568-2