[1]徐 霄,丁天宇,于 威,等.猪圆环病毒的基因密码子偏好性分析[J].中国预防兽医学报,2018,(06):471-475.[doi:0.3969/j.issn.1008-0589.201802007]
 XU Xiao,DING Tian-yu,YU Wei,et al.Analysis of codon usage bias in porcine circovirus gene[J].Chinese journal of preventive veterinary medicine,2018,(06):471-475.[doi:0.3969/j.issn.1008-0589.201802007]
点击复制

猪圆环病毒的基因密码子偏好性分析()
分享到:

《中国预防兽医学报》[ISSN:1008-0589/CN:23-1417/S]

卷:
期数:
2018年06
页码:
471-475
栏目:
病原生物学
出版日期:
2018-06-20

文章信息/Info

Title:
Analysis of codon usage bias in porcine circovirus gene
文章编号:
1008-0589(2018)6-0471-05
作者:
 

徐 霄丁天宇于 威姜永厚全滟平*

 (浙江理工大学 生命科学学院,浙江 杭州310018)
Author(s):
 

XU Xiao DING Tian-yu YU Wei JIANG Yong-hou QUAN Yan-ping*

 (College of Life Science, Zhejiang Sci-Tech University, Hangzhou 310018, China)
关键词:
 猪圆环病毒基因密码子偏好性生物信息学
Keywords:
  porcine circovirus  gene  codon usage bias  bioinformatics
DOI:
0.3969/j.issn.1008-0589.201802007
文献标志码:
A
摘要:
为了解不同型猪圆环病毒(PCV)(PCV1、PCV2、PCV3)的密码子使用特点及其主要影响因素,本研究通过生物信息学方法对3个型PCVs的rep和cap两个基因序列的密码子偏好性进行综合分析。结果显示3个型PCVs间、rep与cap两个基因间、PCVs与宿主间的密码子偏好性均存在明显差异。密码子适应指数(CAI)分析预示3个型PCVs的两个基因在宿主细胞中表达水平低。同义密码子的相对使用频率(RSCU)分析表明PCV1与PCV2具有相似的同义密码子使用模式,而PCV3与PCV1、PCV2存在明显差异,3个型PCVs与宿主的密码子偏好性也存在明显差异。rep基因偏好使用U或G结尾的同义密码子,cap基因偏好使用C结尾的同义密码子。通过中性绘图分析和ENC绘图分析显示,PCV的密码子使用模式受自然选择压力影响大,受突变压力的影响小。本研究为阐明PCV的分子进化规律及病毒对宿主翻译系统的适应性提供重要的实验依据。
  
Abstract:
Based on pathogenicity and antigenicity, porcine circovirus (PCV) is divided into three types: PCV1, PCV2, and PCV3. To investigate codon usage pattern and main influence factor, the codon usage bias of rep and cap genes in three types of PCVs were analyzed with bioinformatic softwares. There were significant differences in the codon usage bias among the three types of PCVs and between PCVs and host. Codon adaptation index analysis predicted that the two PCV genes from three types had low expression levels in host cells. The analysis on relative synonymous codon usage suggested PCV1 had similar synonymous codon usage patterns with PCV2, while PCV3 was apparently different from PCV1 and PCV2. There were significant differences in codon usage bias between the three PCVs and host. rep gene preferred to use U or G-end synonymous codon, whereas cap gene prefered to use C-end synonymous codon. Neutrality plot and ENC plot analysis showed compared to mutation pressure, natural selection played a substantial role in codon usage pattern of PCV. This study provided experimental evidences for elucidating of the molecular evolution rules of PCV and the viral adaptability to the host translation system.

参考文献/References:

[1] Xiao Chao-Ting, Halbur P G, Opriessnig T. Global molecular genetic analysis of porcine circovirus type 2 (PCV2) sequences confirms the presence of four main PCV2 genotypes and reveals a rapid increase of PCV2d [J]. J Gen Virol, 2015, 96(Pt 7):1830-1841.
[2]Phan T G, Giannitti F, Rossow S, et al. Detection of a novel circovirus PCV3 in pigs with cardiac and multi-systemic inflammation [J]. Virol J, 2016, 13(1): 184.
[3]Fan Sheng-xian, Ku Xu-gang, Chen Fang-zhou, et al. Complete genome sequence of a novel porcine circovirus type 3 strain, PCV3/CN/Hubei-618/2016, isolated from China [J]. Genome Announc, 2017, 5(15): e00100-17.
[4]Morozov I, Sirinarumitr T, Sorden S D, et al. Detection of a novel strain of porcine circovirus in pigs with postweaning multisystemic wasting syndrome [J]. J Clin Microbiol, 1998, 36(9): 2535-2541.
[5]Phenix K V, Weston J H, Ypelaar I, et al. Nucleotide sequence analysis of a novel circovirus of canaries and its relationshipto other members of the genus Circovirus of the family Circoviridae[J]. J Gen Virol, 2001, 82(Pt 11): 2805-2809.
[6]Sharp P M, Li W H. An evolutionary perspective on synonymous codon usage in unicellular organisms [J]. J Mol Evol, 1986, 24(1-2): 28-38.
[7]Sueoka N, Kawanishi Y. DNA G+C content of the third codon position and codon usage biases of human genes [J]. Gene, 2000, 261(1): 53-62.
[8]Wright F. The ’effective number of codons’ used in a gene [J]. Gene, 1990, 87(1): 23-29.
[9]Palinski R, Pi?觡eyro P, Shang P, et al. A novel porcine circovirus distantly related to known circoviruses is associated with porcine dermatitis and nephropathy syndrome and reproductive failure [J]. J Virol, 2016, 91(1)pii: e01879-16. 
[10]Tischer I, Peters D, Rasch R, et al. Replication of porcine cireovirus: induction by glueosamine and cell cycle dependence [J]. Arch Virol, 1987, 96: 39-57.
[11]Meerts P, Misinzo G, McNeilly F, et al. Replication kinetics of different porcine circovirus 2 strains in PK-15 cells, fetal cardiomyocytes and macrophages [J]. Arch Virol, 2005, 150: 427-441.
[12]Wang Hong-ju, Liu Si-qing, Zhang Bo, et al. Analysis of synonymous codon usage bias of Zika virus and its adaption to the hosts [J]. PLoS One, 2017, 12(1): e0170128.
[13]Chen Ye, Shi Yu-zhen, Deng Hong-juan, et al. Characterization of the porcine epidemic diarrhea virus codon usage bias [J]. Infect Genet Evol, 2014, 28: 95-100.
[14]Yin Xin, Lin Yue-zhi, Cai Wei-gang, et al. Comprehensive analysis of the overall codon usage patterns in equine infectious anemia virus [J]. Virol J, 2013, 10: 356.
(本文编辑:彭永刚) 

相似文献/References:

[1]梁化春,齐景伟,刘淑英*,等.绵羊肺腺瘤病的病理学及RT-PCR诊断 [J].中国预防兽医学报,2009,(06):443.
 LIANG Hua-chun,QI Jing-wei,LIU Shu-ying*,et al.The pathological and RT-PCR diagnosis ofsheep pulmonary adenomatosis [J].Chinese journal of preventive veterinary medicine,2009,(06):443.
[2]刘合义,孙留霞,王进轶,等.牛冠状病毒重组N蛋白间接ELISA检测方法的建立 [J].中国预防兽医学报,2009,(08):618.
 LIU He-yi,SUN Liu-xia,WANG Jin-yi,et al.Development of an indirect ELISA for the detectionof Bovine coronavirus using recombinant N protein [J].Chinese journal of preventive veterinary medicine,2009,(06):618.
[3]杨 鸿,林 涛,邓 桦,等.免疫组化Envision法检测肺组织中猪圆环病毒抗原的研究 [J].中国预防兽医学报,2009,(09):698.
 YANG Hong,LIN Tao,DENG Hua,et al.Detection of porcine circovirus antigen in lung tissue of swine by Envision method[J].Chinese journal of preventive veterinary medicine,2009,(06):698.
[4]姜永厚,商晗武,徐 辉,等.基于多重PCR的寡核苷酸基因芯片检测猪瘟病毒,猪繁殖与呼吸障碍综合征病毒及猪圆环病毒1型和2型[J].中国预防兽医学报,2010,(03):194.
 JIANG Yong-hou,SHANG Han-wu,XU Hui,et al.A multiplex PCR based oligonucleotide microarray for detection and differentiation of classical swine fever virus, porcine reproductive and respiratory virus and porcine circovirus types 1 and 2[J].Chinese journal of preventive veterinary medicine,2010,(06):194.
[5]成大荣,朱善元,陈长春,等.猪圆环病毒1型和2型衣壳蛋白的表达与鉴定[J].中国预防兽医学报,2008,(10):760.
 CHENG Da-rong,ZHU Shan-yuan,CHEN Chang-chun,et al.Expression and identification of the capsid protein of porcine circovirus[J].Chinese journal of preventive veterinary medicine,2008,(06):760.
[6]刘建波,郭龙军,危艳武,等.猪输血传播病毒(TTV)与猪圆环病毒混合感染的检测及TTV遗传变异分析[J].中国预防兽医学报,2011,(01):6.[doi:10.3969/j.issn.1008-0589.2011.01.02]
 LIU Jian-bo,GUO Long-jun,WEI Yan-wu,et al.Detection of co-infection of porcine torque teno virus (TTV) and porcine circovrius and genetic variation analysis for TTV[J].Chinese journal of preventive veterinary medicine,2011,(06):6.[doi:10.3969/j.issn.1008-0589.2011.01.02]
[7]王生育,颜江华,孔繁德*,等.猪圆环病毒2型ORF1和ORF2基因的克隆与表达[J].中国预防兽医学报,2007,(12):934.
 WANG Sheng-yu,YAN Jiang-hua,KONG Fan-de*,et al.Cloning and expression of ORF1 and ORF2 genes of porcine circovirus type 2[J].Chinese journal of preventive veterinary medicine,2007,(06):934.
[8]崔尚金,全滟平,李 曦,等.猪圆环病毒间接免疫荧光方法的建立[J].中国预防兽医学报,2007,(01):63.
 CUI Shang-jin,QUAN Yan-ping,LI Xi,et al.The development of an indirect immunofluorescent technique of porcine circovirus[J].Chinese journal of preventive veterinary medicine,2007,(06):63.
[9]李 杰,葛 猛,罗 维,等.猪圆环病毒2型Rep蛋白ELISA抗体检测方法的建立[J].中国预防兽医学报,2012,(11):894.[doi:doi: 10.3969/j.issn.1008-0589.2012.11.11]
 LI Jie,GE Meng,LUO Wei,et al.Development of an indirect ELISA for detecting antibodies against porcine circovirus 2 based on recombinant Rep protein[J].Chinese journal of preventive veterinary medicine,2012,(06):894.[doi:doi: 10.3969/j.issn.1008-0589.2012.11.11]
[10]秦玉寅,王雪峰,韦华冕,等.马传染性贫血病毒弱毒疫苗gp90多样性及其对病毒体外增殖的影响[J].中国预防兽医学报,2014,(03):182.[doi:10.3969/j.issn.1008-0589.2014.03.04]
 QIN Yu-yin,WANG Xue-feng,WEI Hua-mian,et al.gp90 genetic diversity of EIAV attenuated vaccine and its impact on EIAV’s proliferation in vitro[J].Chinese journal of preventive veterinary medicine,2014,(06):182.[doi:10.3969/j.issn.1008-0589.2014.03.04]
[11]徐文娟,张瑛杰,李青青,等.利用细菌展示技术系统地筛选猪圆环病毒2型衣壳蛋白的线性抗原区域[J].中国预防兽医学报,2016,(05):398.[doi:10.3969/j.issn.1008-0589.2016.05.13]
 XU Wen-juan,ZHANG Ying-jie,LI Qing-qing,et al. Systematic mapping the linear antigenic domains of the porcine circovirus 2b Cap protein by bacterial display technology[J].Chinese journal of preventive veterinary medicine,2016,(06):398.[doi:10.3969/j.issn.1008-0589.2016.05.13]

更新日期/Last Update: 2018-07-11