摘要
【目的】分析黄病毒科瘟病毒属的猪瘟病毒(CSFV)、牛病毒性腹泻病毒(BVDV)和羊边界病毒(BDV)3种病毒多聚蛋白酶基因密码子的使用特点,初步探讨3种病毒多聚蛋白酶基因的进化及对不同宿主的适应策略。【方法】运用EMBOSS软件的CHIPS和CUSP程序及CodonW在线分子生物学软件,分析CSFV、BVDV和BDV的有效密码子数(ENc),碱基GC含量(Gcall),密码子第1、2、3位GC含量(GC1、GC2、GC3),相对同义密码子使用度(RSCU)及同义密码子第3位的GC含量(GC3s),并对3种病毒多聚蛋白酶基因的ENc进行绘图分析。【结果】CSFV、BVDV、BDV 3种病毒多聚蛋白酶基因的ENc值分别为51.205,51.323和52.580,表明3种病毒多聚蛋白酶基因的密码子偏好程度均较低;上述3种病毒多聚蛋白酶基因的GC含量分别为46.84%,45.99%和45.71%,均不超过50%;除BDV多聚蛋白酶基因同义密码子含量表现为GC1>GC3>GC2外,CSFV和BVDV均表现为GC3>GC1>GC2,且除CSFV的GC3为52.02%外,所有病毒的GC1、GC2、GC3均小于50%,可见3种病毒间的碱基组成(GC含量)及ENc值差异较小。RSCU分析表明,与CSFV偏爱使用G/C结尾的密码子不同,BVDV和BDV更偏爱使用以A结尾的密码子,这可能与病毒对宿主的适应策略有关。ENc绘图分析(Nc-plot)说明,碱基组成对密码子使用模式影响较小。【结论】CSFV、BVDV、BDV 3种病毒多聚蛋白酶基因密码子的偏好性较低,这可能是病毒进化过程中对宿主的一种适应策略。
【Objective】This study analyzed the application characteristics of poly protease gene codons of classical swine fever virus(CSFV),bovine viral diarrhea virus(BVDV)and sheep boundary virus(BDV)and discussed their evolution and adaptive strategies for different hosts.【Method】Effective number of codons(ENc),GC contents,GC contents of synonymous codons at 1st,2nd,and 3rd positions,relative synonymous codon usage(RSCU)and GC3 sof CSFV,BVDV and BDV were analyzed using CHIPS and CUSP programs of EMBOSS(European Molecular Biology Open Software Suite)and CodonW software.Meanwhile,poly protease genes of the three viruses were analyzed by ENc plotting.【Result】The ENc values of poly protease genes of CSFV,BVDV,and BDV were 51.205,51.323 and 52.580,respectively,indicating that the codon preferences of poly protease genes of the three viruses were all low.GC contents of them were 46.84%,45.99%,and 45.71%,respectively.Synonymous codons contents of BDV poly protease gene were in a decreasing order of GC1>GC3>GC2,while those of CSFV and BVDV were in a decreasing order of GC3>GC1>GC2.All GC contents of GC1,GC2,and GC3 were lower than 50%,except GC3 of CSFV(52.02%).The differences in base compositions of the three viruses and ENc values were small.RSCU analysis showed that CSFV was different from BVDV and BDV,CSFV preferred to use G or C ending codons,while BVDV and BDV preferred to use A ending codons.This may be related to virus host adaptation strategies.ENc plots(Nc-plot)showed that base composition had little effect on the codon usage patterns.【Conclusion】The condon preferences of poly protease genes of CSFV,BVDV,and BDV were low,which may be related to their host adaptation strategies.
出处
《西北农林科技大学学报（自然科学版）》
CSCD
北大核心
2015年第1期7-13,共7页
Journal of Northwest A&F University(Natural Science Edition)
基金
新疆生产建设兵团国际科技合作计划项目(2012BC006)
公益性行业(农业)科研专项子课题项目(201303037-5)
关键词
黄病毒科瘟病毒属
多聚蛋白酶基因
同义密码子
偏爱性
Pestivirus genus of the family Flaviviridae
poly protease gene
synonymous codon
preference
