title: Analysis of synonymous codon usage pattern in duck circovirus.
abstract: Duck circovirus (DuCV) disease causes a long-term immunosuppressive and multiple secondary infection in ducks. In this study, relative synonymous codon usage (RSCU) values, nucleotide contents and effective number of codon (ENC) values were calculated and compared among open reading frames (ORFs) of 53 DuCV genomes. The results reveal that most of the codons are ended with C and the overall bias is not remarkable in DuCV. A comparative analysis of codon contents and ENC values indicates that mutation pressure is the most significant factor responsible for the evolutional processes of codon usage bias in DuCV. However, other factors, such as composition constraints, translation selection, hydrophobicity and aromaticity should not be ignored. Finally principal component analysis (PCA) and hierarchical clustering method were performed based on RSCU. The significant difference of codon usage bias exists in DuCV-1 and DuCV-2 genotypes, but codon usage pattern of DuCV from the different epidemic areas or subtypes fails to influence the formation of codon usage bias. Analysis of the relationship of synonymous codon usage variation based on the two genotypes suggests that DuCV-2 is more conservative than DuCV-1, which may because of recombination events. Moreover, there are distinct differences in the degree of codon usage pattern evolution in different function genes, rep and cap. Therefore, the genotypes, subtypes and different functional genes also relate to the pattern of synonymous codon usage. The main objective of this study is to provide some sight into synonymous codon usage characteristics and the evolutionary relationship of DuCV.
authors.affiliation: Avian Disease Research Center, Sichuan Agricultural University, Chengdu 611130, China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan 611130, China. Electronic address: xyxlxun@163.com.
authors.forename: Yu
authors.initials: Y
authors.lastname: Xu
authors.affiliation: Avian Disease Research Center, Sichuan Agricultural University, Chengdu 611130, China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan 611130, China. Electronic address: jiary@sicau.edu.cn.
authors.forename: Renyong
authors.initials: R
authors.lastname: Jia
authors.affiliation: Avian Disease Research Center, Sichuan Agricultural University, Chengdu 611130, China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan 611130, China. Electronic address: zhangzhilong0518@163.com.
authors.forename: Zhilong
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Avian Disease Research Center, Sichuan Agricultural University, Chengdu 611130, China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan 611130, China. Electronic address: lu_yanyan5@163.com.
authors.forename: Yanyan
authors.initials: Y
authors.lastname: Lu
authors.affiliation: Avian Disease Research Center, Sichuan Agricultural University, Chengdu 611130, China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan 611130, China. Electronic address: mshwang@163.com.
authors.forename: Mingshu
authors.initials: M
authors.lastname: Wang
authors.affiliation: Avian Disease Research Center, Sichuan Agricultural University, Chengdu 611130, China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan 611130, China. Electronic address: zdk24@sicau.edu.cn.
authors.forename: Dekang
authors.initials: D
authors.lastname: Zhu
authors.affiliation: Avian Disease Research Center, Sichuan Agricultural University, Chengdu 611130, China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan 611130, China. Electronic address: sophia_cs@163.com.
authors.forename: Shun
authors.initials: S
authors.lastname: Chen
authors.affiliation: Avian Disease Research Center, Sichuan Agricultural University, Chengdu 611130, China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan 611130, China. Electronic address: liumafengra@163.com.
authors.forename: Mafeng
authors.initials: M
authors.lastname: Liu
authors.affiliation: Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan 611130, China. Electronic address: yinzhongq@163.com.
authors.forename: Zhongqiong
authors.initials: Z
authors.lastname: Yin
authors.affiliation: Avian Disease Research Center, Sichuan Agricultural University, Chengdu 611130, China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan 611130, China. Electronic address: chenganchun@vip.163.com.
authors.forename: Anchun
authors.initials: A
authors.lastname: Cheng
mesh_terms: D001482:Base Composition; D017925:Circovirus / Q000235:genetics*; D016000:Cluster Analysis; D003062:Codon; D019143:Evolution, Molecular; D016679:Genome, Viral; D008957:Models, Genetic; D016366:Open Reading Frames; D025341:Principal Component Analysis
chemical_list: D003062:Codon
keywords: Codon usage pattern; Duck circovirus; Mutation pressure; Recombination events