title: First analysis of synonymous codon usage in porcine circovirus.
abstract: Porcine circovirus (PCV) is grouped into two types: PCV1 and PCV2. PCV1 is isolated from cultured cells and usually causes no clinical diseases in pigs. PCV2 is a pathogen of severe pig disease and a great threat to swine health and production. In our study, to investigate the codon usage bias of PCV, the genomic sequences of PCV1 and PCV2 were analyzed. The results showed that the codon usage bias of PCV was very low. An effective number of codons (ENC) plot analysis indicated that mutational pressure influences the codon usage bias of PCV. Neutrality plot analysis showed that mutation bias dominated over natural selection in shaping the codon usage bias of PCV1, but mutation bias and natural selection contributed equally to the codon usage bias of PCV2. Principal component analysis showed that different ORFs and dinucleotide patterns were also factors influencing the codon usage bias of PCV. Our study is helpful in understanding the codon usage pattern of PCV and the evolution of PCV.
authors.affiliation: Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.
authors.forename: Ye
authors.initials: Y
authors.lastname: Chen
authors.forename: Jingchen
authors.initials: J
authors.lastname: Sun
authors.forename: Xiong
authors.initials: X
authors.lastname: Tong
authors.forename: Jian
authors.initials: J
authors.lastname: Xu
authors.forename: Hongjuan
authors.initials: H
authors.lastname: Deng
authors.forename: Zhiguo
authors.initials: Z
authors.lastname: Jiang
authors.forename: Chengfeng
authors.initials: C
authors.lastname: Jiang
authors.forename: Junli
authors.initials: J
authors.lastname: Duan
authors.forename: Jingcong
authors.initials: J
authors.lastname: Li
authors.forename: Pei
authors.initials: P
authors.lastname: Zhou
authors.forename: Chong
authors.initials: C
authors.lastname: Wang
mesh_terms: D000818:Animals; D001483:Base Sequence; D018173:Circoviridae Infections / Q000662:veterinary* / Q000821:virology; D017925:Circovirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D003062:Codon; D019143:Evolution, Molecular; D016679:Genome, Viral; D008969:Molecular Sequence Data; D009154:Mutation; D013552:Swine; D013553:Swine Diseases / Q000821:virology*
chemical_list: D003062:Codon