title: Time-calibrated phylogenomics of the classical swine fever viruses: genome-wide bayesian coalescent approach.
abstract: The phylogeny of classical swine fever virus (CSFV), the causative agent of classical swine fever (CSF), has been investigated extensively. However, no evolutionary research has been performed using the whole CSFV genome. In this study, we used 37 published genome sequences to investigate the time-calibrated phylogenomics of CSFV. In phylogenomic trees based on Bayesian inference (BI) and Maximum likelihood (ML), the 37 isolates were categorized into five genetic types (1.1, 1.2, 2.1, 2.3, and 3.4). Subgenotype 1.1 is divided into 3 groups and 1 unclassified isolate, 2.1 into 4 groups, 2.3 into 2 groups and 1 unclassified isolate, and subgenotype 1.2 and 3.4 consisted of one isolate each. We did not observe an apparent temporal or geographical relationship between isolates. Of the 14 genomic regions, NS4B showed the most powerful phylogenetic signal. Results of this evolutionary study using Bayesian coalescent approach indicate that CSFV has evolved at a rate of 13×.010-4 substitutions per site per year. The most recent common ancestor of CSFV appeared 2770.2 years ago, which was about 8000 years after pig domestication. The effective population size of CSFV underwent a slow increase until the 1950s, after which it has remained constant.
authors: Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
authors: Taehyung
authors: T
authors: Kwon
authors: Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
authors: Sook Hee
authors: SH
authors: Yoon
authors: Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-747, Republic of Korea.
authors: Kyu-Won
authors: KW
authors: Kim
authors: Department of Animal Sciences, University of Illinois, Urbana, IL, 61801, United States of America.
authors: Kelsey
authors: K
authors: Caetano-Anolles
authors: C&K Genomics Inc. 514 Main Bldg., Seoul National University Research Park, San 4-2 Boncheon-dong, Gwanak-gu, Seoul, 151-919, Republic of Korea.
authors: Seoae
authors: S
authors: Cho
authors: Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
authors: Heebal
authors: H
authors: Kim
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D006691:Classical Swine Fever / Q000821:virology; D006692:Classical Swine Fever Virus / Q000145:classification* / Q000235:genetics*; D016679:Genome, Viral; D009154:Mutation; D010802:Phylogeny; D012367:RNA, Viral / Q000032:analysis*; D012641:Selection, Genetic; D017423:Sequence Analysis, RNA / Q000379:methods*; D013552:Swine
chemical_list: D012367:RNA, Viral