title: Analysis of full-length genomes of porcine teschovirus (PTV) and the effect of purifying selection on phylogenetic trees.
abstract: To study the outcome of natural selection using phylogenetic trees, we analyzed full-length genome sequences of porcine teschovirus (PTV). PTV belongs to the family Picornaviridae and has a positive-stranded RNA genome, the replication of which is carried out by the error-prone viral RNA-dependent RNA polymerase. The viral RNA encodes a single polyprotein that is cleaved into structural (i.e., L, VP4, VP2, VP3 and VP1) and nonstructural proteins (i.e., 2A, 2B, 2C, 3A, 3B, and 3C). A high degree of genetic diversity was found based on the pairwise nucleotide distances and on the mean ratio of the number of nonsynonymous (dN) and synonymous (dS) substitutions (dN/dS) in the structural genes. Conversely, the diversity of the nonstructural genes was lower. The differences in genetic diversity between the structural and nonstructural genomic regions were likely due to strong purifying selection; consequently, the estimates of phylogenies were also discordant among these genes. In particular, maximum-likelihood and Bayesian methods generated short-branched trees when loci that are under strong purifying selection were used. These findings indicate that even in an RNA virus with an intrinsically high mutation rate, a strong purifying selection will curb genetic diversity and should be considered an important source of bias in future studies based on phylogenetic methods.
authors: Instituto de Ciências Biológicas, Federal University of Pará, Avenida Augusto Corrêa, 1, CEP 66075-000, Belém, Pará, Brazil.
authors: Fabiola
authors: F
authors: Villanova
authors: Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences, Beijing, 100094, China.|State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, 427 Maduan Street, Nangang, Harbin, 150001, China.
authors: Shangjin
authors: S
authors: Cui
authors: College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, China.
authors: Xia
authors: X
authors: Ai
authors: Instituto de Ciências Biológicas, Federal University of Pará, Avenida Augusto Corrêa, 1, CEP 66075-000, Belém, Pará, Brazil. elcioleal@gmail.com.
authors: Élcio
authors: É
authors: Leal
mesh_terms: D019143:Evolution, Molecular; D005814:Genes, Viral / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics; D016679:Genome, Viral / Q000235:genetics*; D010802:Phylogeny; D011995:Recombination, Genetic / Q000235:genetics; D016415:Sequence Alignment; D052700:Teschovirus / Q000235:genetics* / Q000302:isolation & purification