title: Characterization of the porcine epidemic diarrhea virus codon usage bias.
abstract: Porcine epidemic diarrhea virus (PEDV) has been responsible for several recent outbreaks of porcine epidemic diarrhea (PED) and has caused great economic loss in the swine-raising industry. Considering the significance of PEDV, a systemic analysis was performed to study its codon usage patterns. The relative synonymous codon usage value of each codon revealed that codon usage bias exists and that PEDV tends to use codons that end in T. The mean ENC value of 47.91 indicates that the codon usage bias is low. However, we still wanted to identify the cause of this codon usage bias. A correlation analysis between the codon compositions (A3s, T3s, G3s, C3s, and GC3s), the ENC values, and the nucleotide contents (A%, T%, G%, C%, and GC%) indicated that mutational bias plays role in shaping the PEDV codon usage bias. This was further confirmed by a principal component analysis between the codon compositions and the axis values. Using the Gravy, Aroma, and CAI values, a role of natural selection in the PEDV codon usage pattern was also identified. Neutral analysis indicated that natural selection pressure plays a more important role than mutational bias in codon usage bias. Natural selection also plays an increasingly significant role during PEDV evolution. Additionally, gene function and geographic distribution also influence the codon usage bias to a degree.
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.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: Yuzhen
authors.initials: Y
authors.lastname: Shi
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: Hongjuan
authors.initials: H
authors.lastname: Deng
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: Ting
authors.initials: T
authors.lastname: Gu
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: Jian
authors.initials: J
authors.lastname: Xu
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: Jinxin
authors.initials: J
authors.lastname: Ou
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: Zhiguo
authors.initials: Z
authors.lastname: Jiang
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: Yiren
authors.initials: Y
authors.lastname: Jiao
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: Tan
authors.initials: T
authors.lastname: Zou
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. Electronic address: betty@scau.edu.cn.
authors.forename: Chong
authors.initials: C
authors.lastname: Wang
mesh_terms: D000818:Animals; D001482:Base Composition; D003062:Codon; D018352:Coronavirus Infections / Q000662:veterinary; D019143:Evolution, Molecular; D016679:Genome, Viral; D005838:Genotype; D009154:Mutation; D053485:Porcine epidemic diarrhea virus / Q000235:genetics*; D012641:Selection, Genetic; D013552:Swine / Q000821:virology; D013553:Swine Diseases / Q000453:epidemiology / Q000821:virology
chemical_list: D003062:Codon
keywords: Codon usage bias; Mutation bias; Natural selection; Porcine epidemic diarrhea virus