Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model

BMC Evolutionary Biology

Research Article

Chi Pang Li¹  Ka Hou Chu¹  Roger Wei Wang²  Vo Anh³  Zu-Guo Yu⁴  Li-Qian Zhou⁵ 

[1] Department of Biology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China;Department of Mathematics, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China;School of Mathematical Sciences, Queensland University of Technology, GPO Box 2434, Q 4001, Brisbane, Australia;School of Mathematical Sciences, Queensland University of Technology, GPO Box 2434, Q 4001, Brisbane, Australia;School of Mathematics and Computational Science, Xiangtan University, 411105, Hunan, China;School of Mathematics and Computational Science, Xiangtan University, 411105, Hunan, China;

关键词: White Spot Syndrome Virus;    African Swine Fever Virus;    Composition Vector;    Bocavirus;    Genome Tree;   

DOI  :  10.1186/1471-2148-10-192

 received in 2009-09-25, accepted in 2010-06-22,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundThe vast sequence divergence among different virus groups has presented a great challenge to alignment-based analysis of virus phylogeny. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignment could not be directly applied to the whole-genome comparison and phylogenomic studies of viruses. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among the alignment-free methods, a dynamical language (DL) method proposed by our group has successfully been applied to the phylogenetic analysis of bacteria and chloroplast genomes.ResultsIn this paper, the DL method is used to analyze the whole-proteome phylogeny of 124 large dsDNA viruses and 30 parvoviruses, two data sets with large difference in genome size. The trees from our analyses are in good agreement to the latest classification of large dsDNA viruses and parvoviruses by the International Committee on Taxonomy of Viruses (ICTV).ConclusionsThe present method provides a new way for recovering the phylogeny of large dsDNA viruses and parvoviruses, and also some insights on the affiliation of a number of unclassified viruses. In comparison, some alignment-free methods such as the CV Tree method can be used for recovering the phylogeny of large dsDNA viruses, but they are not suitable for resolving the phylogeny of parvoviruses with a much smaller genome size.

【 授权许可】

Unknown   
© Yu et al; licensee BioMed Central Ltd. 2010. This article is published under license to 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.