水稻条纹病毒致病性分化与分子变异
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摘要
以灰飞虱为介体昆虫,将水稻条纹病毒(Rice stipe virus,RSV)23个代表分离物接种于水稻品种武育粳3号、合系39、花优63。根据株发病率,23个分离物的致病型可分为5个等级,分别为强致病型、次强致病型、中致病型、弱致病型、极弱致病型。致病分化表现在地理、株系及水稻品种等三个方面的差异。分析表明,不同分离物在发病率、发病时间、症状表现及对介体灰飞虱传毒影响上存在差异;以地理划分的云南自然种群和云南外自然种群在致病上存在明显的差异。云南自然种群以弱致病型为主,但间或有强致病型分离物;云南外自然种群存在强致病型分离物,属于混合致病群,致病型多样化。YBS07分离物在水稻品种上的发病时间、症状表现以及对灰飞虱传毒效率影响上的数据都接近或超过云南外分离物,是云南种群中隐藏的强致病型分离物。致病性结构与病害流行的关系提示病害防治要采取针对性措施。
对8个致病性存在差异的代表分离物的遗传变异分析表明,基因组不同片段表现出不同的变异特征;云南分离物与云南外分离物在遗传关系上具有明显的差异;YBS07在遗传关系上介于云南分离物与云南外分离物间,但更靠近云南分离物。遗传多样性分析表明,致病性相对较弱的云南分离物对应的RdRp、NS3、SP、NSvc4等4个基因比云南外分离物受到更大的负选择压力。YBS07分离物在基因的多样性上介于云南分离物与云南外分离物间,但更靠近云南分离物。对RSV种群遗传距离分析表明,RSV中国种群可以划分为云南亚群、云南外亚群以及由云南亚群中分化出来的混合亚群等三个亚群;云南与云南外两个自然种群存在相互侵染现象。种群遗传多样性分析显示,RSV的7个基因受到强烈的负选择压力。在遗传多样性上: NS2>NS3>CP>NSvc2>SP>NSvc4>RdRp ;在保守性上:RdRp>NSvc4>SP>NSvc2>CP>NS3>NS2。对IR4遗传距离的分析也表明混合亚群及两个自然种群相互侵染现象的存在;RSV三种类型IR4的进化经历了两次分化与两次分离。
序列分析显示,RSV基因组的末端非编码区域高度保守,差异主要存在于云南分离物与云南外分离物之间;末端序列能形成稳定的发夹结构。对RSV编码的7个蛋白氨基酸序列分析显示,RdRp蛋白存在跨膜区段、卷曲螺旋结构、以及短链脱氢还原酶家族信号等多个功能位点;NS2蛋白存在强烈的内部信号肽裂解位点;NSvc2存在N端信号肽、强烈的内部信号肽裂解位点,具有膜蛋白属性;NS3蛋白存在一段卷曲螺旋结构及多个功能位点,云南4个分离物C末端的疏水性明显强于YCX1以及云南外分离物;CP蛋白存在一段卷曲螺旋结构及多个功能位点;SP、NSvc4蛋白分别存在一个内部信号肽裂解位点、一个跨膜区段及多个功能位点。终止密码子分析表明,RSV偏爱使用UAG作为终止密码子;云南分离物与云南外分离物在终止密码子使用上存在差异。对基因间隔区分析表明,RNA2-4的基因间隔区存在正向重复序列、反向重复序列;IR3、IR4还存在明显的插入或缺失序列;IR2-4均能形成稳定的大发夹结构。
测序鉴定RSV云南楚雄分离物一个重组RNA,即YCX07R,由RSV的RNA2的与RNA3重组而成。序列分析显示,YCX07R具有RSV基因组结构特征,其两个末端的序列互补。在正义链及反义链上均存在一个开放阅读框,分别编码YCX07R-5P及YCX07R-3P。分析推测重组系由RNA流产性复制引起或重组的两个片段通过重组点联结形成。
Tweenty-three isolates of Rice stripe virus (RSV) from Yunnan, Jiangsu, Shandong, Henan, and Anhui provinces were inoculated to rice varieties by landelphax striatellus.According to the morbidity, tweenty-three isolates could be divided into five grades, namely strong virus(sv), semi-strong virus(ss), middle strong virus(ms), weak virus(wv) and least weak virus(lw). Pathogenicity differentiation correlated with geographic distribution, strain differences and rice varieties. There were differences among isolates in the morbidity, time to exhibit disease, symptom and influences to landelphax striatellus’s transmission.Two nature populations, Yunnan(YN) and out of Yunnan(OY), showed obvious different pathogenicity too. Some strong virus screened, more weak virus composed the population YN.Pupulation OY had more strong virus than YN and belong to mixed and variant population of five grades. The isolate of YBS07 showed stong pathogenicity similar to OY in the time to exhibit disease, symptom and influences to landelphax striatellus’s transmission. The relationship between pathogenicity differentiation and epidemic of diseases suggested that specific measures should be taken in disease prevention and control.
The genomes of eight representative isolates on pathogenicity were sequenced.Analysis of genetic variation showed that different fragment display different variant feature, that isolates of YN differed from isolates of OY in genetic relations obviously and that YBS07 isolate conducted genetic relations between YN and OY with trending to YN. Analysis of genetic diversity indicat that four weak isolates of YN were compressed by more negative selection pressure than the other four isolates of OY in RdRp、NS3、SP and NSvc4.The genetic diversity of YBS07 was between YN and OY with trending to YN.Analysis of population genetic distance display that the RSV population in china can divided into three subgroups,Yunnan subgroup,out of Yunnan subgroup, mixed subgroup originated from Yunnan group.There existed invasion between YN and OY. Analysis of population genetic diversity showed that seven genes of RSV were compressed strong negetive selection pressure with NS2>NS3>CP>NSvc2>SP>NSvc4>RdRp in genetic diversity and RdRp>NSvc4 >SP>NSvc2>CP>NS3>NS2 in conservation.The analysis of genetic diatance of IR4 also showed that there existed mixed subgroup and invasion between YN and OY.Three types of IR4 experienced two differentiations and two separations.
Analysis of sequence showed that the terminal untrantion regions(UTR) of genome of RSV had hight conservation,with variation between YN an OY. The UTR could form stable hairpin structure.Analysis of amino acid sequence showed that RdRp had transmembrane segments, coiled coils and some protein functional sites such as short-chain dehydrogenases/reductases family signature.NS2 had a strong potential cleavage site of signal peptide.NSvc2 had an N-signal peptide, a strong potential cleavage site of signal peptide and the property of membrane protein. NS3 had a coiled coil, some protein functional sites, and a differences of C-terminal hydrophobicity between YN and OY.CP had a coiled coil and some protein functional sites. SP and NSvc4 both had a potential cleavage site of signal peptide,a transmembrane segment and somes protein functional sites.Analysis of stop codons indicated that RSV prefers to use UAG as the stop codon and there are differences on preference of stop codon between YN and OY. Analysis of sequence showed that IR2-4 had direct repeat fragments and inverted repeat fragments, those could formed stable hairpin structure. IR3 and IR4 even had obvious insert and missing sequences.
A recombinant RNA of one isolate of Rice stripe virus(RSV) from Chuxiong(YCX07), Yunnan province, China, was sequenced. The RNA(YCX07R) was recombined from the 3' segments of RNA2 and RNA3 of RSV. The recombinant RNA uses ambisense coding strategy and encodes two proteins, namely YCX07R-5P and YCX07R-3P. The two proteins located on the 5' end of the plus and minus strand, respectively. This is similar to the four RNAs of RSV. It was discussed that the RNA was recombined from abortion replication or linked by two recombinant fragments through the recombinant site directly.
对8个致病性存在差异的代表分离物的遗传变异分析表明,基因组不同片段表现出不同的变异特征;云南分离物与云南外分离物在遗传关系上具有明显的差异;YBS07在遗传关系上介于云南分离物与云南外分离物间,但更靠近云南分离物。遗传多样性分析表明,致病性相对较弱的云南分离物对应的RdRp、NS3、SP、NSvc4等4个基因比云南外分离物受到更大的负选择压力。YBS07分离物在基因的多样性上介于云南分离物与云南外分离物间,但更靠近云南分离物。对RSV种群遗传距离分析表明,RSV中国种群可以划分为云南亚群、云南外亚群以及由云南亚群中分化出来的混合亚群等三个亚群;云南与云南外两个自然种群存在相互侵染现象。种群遗传多样性分析显示,RSV的7个基因受到强烈的负选择压力。在遗传多样性上: NS2>NS3>CP>NSvc2>SP>NSvc4>RdRp ;在保守性上:RdRp>NSvc4>SP>NSvc2>CP>NS3>NS2。对IR4遗传距离的分析也表明混合亚群及两个自然种群相互侵染现象的存在;RSV三种类型IR4的进化经历了两次分化与两次分离。
序列分析显示,RSV基因组的末端非编码区域高度保守,差异主要存在于云南分离物与云南外分离物之间;末端序列能形成稳定的发夹结构。对RSV编码的7个蛋白氨基酸序列分析显示,RdRp蛋白存在跨膜区段、卷曲螺旋结构、以及短链脱氢还原酶家族信号等多个功能位点;NS2蛋白存在强烈的内部信号肽裂解位点;NSvc2存在N端信号肽、强烈的内部信号肽裂解位点,具有膜蛋白属性;NS3蛋白存在一段卷曲螺旋结构及多个功能位点,云南4个分离物C末端的疏水性明显强于YCX1以及云南外分离物;CP蛋白存在一段卷曲螺旋结构及多个功能位点;SP、NSvc4蛋白分别存在一个内部信号肽裂解位点、一个跨膜区段及多个功能位点。终止密码子分析表明,RSV偏爱使用UAG作为终止密码子;云南分离物与云南外分离物在终止密码子使用上存在差异。对基因间隔区分析表明,RNA2-4的基因间隔区存在正向重复序列、反向重复序列;IR3、IR4还存在明显的插入或缺失序列;IR2-4均能形成稳定的大发夹结构。
测序鉴定RSV云南楚雄分离物一个重组RNA,即YCX07R,由RSV的RNA2的与RNA3重组而成。序列分析显示,YCX07R具有RSV基因组结构特征,其两个末端的序列互补。在正义链及反义链上均存在一个开放阅读框,分别编码YCX07R-5P及YCX07R-3P。分析推测重组系由RNA流产性复制引起或重组的两个片段通过重组点联结形成。
Tweenty-three isolates of Rice stripe virus (RSV) from Yunnan, Jiangsu, Shandong, Henan, and Anhui provinces were inoculated to rice varieties by landelphax striatellus.According to the morbidity, tweenty-three isolates could be divided into five grades, namely strong virus(sv), semi-strong virus(ss), middle strong virus(ms), weak virus(wv) and least weak virus(lw). Pathogenicity differentiation correlated with geographic distribution, strain differences and rice varieties. There were differences among isolates in the morbidity, time to exhibit disease, symptom and influences to landelphax striatellus’s transmission.Two nature populations, Yunnan(YN) and out of Yunnan(OY), showed obvious different pathogenicity too. Some strong virus screened, more weak virus composed the population YN.Pupulation OY had more strong virus than YN and belong to mixed and variant population of five grades. The isolate of YBS07 showed stong pathogenicity similar to OY in the time to exhibit disease, symptom and influences to landelphax striatellus’s transmission. The relationship between pathogenicity differentiation and epidemic of diseases suggested that specific measures should be taken in disease prevention and control.
The genomes of eight representative isolates on pathogenicity were sequenced.Analysis of genetic variation showed that different fragment display different variant feature, that isolates of YN differed from isolates of OY in genetic relations obviously and that YBS07 isolate conducted genetic relations between YN and OY with trending to YN. Analysis of genetic diversity indicat that four weak isolates of YN were compressed by more negative selection pressure than the other four isolates of OY in RdRp、NS3、SP and NSvc4.The genetic diversity of YBS07 was between YN and OY with trending to YN.Analysis of population genetic distance display that the RSV population in china can divided into three subgroups,Yunnan subgroup,out of Yunnan subgroup, mixed subgroup originated from Yunnan group.There existed invasion between YN and OY. Analysis of population genetic diversity showed that seven genes of RSV were compressed strong negetive selection pressure with NS2>NS3>CP>NSvc2>SP>NSvc4>RdRp in genetic diversity and RdRp>NSvc4 >SP>NSvc2>CP>NS3>NS2 in conservation.The analysis of genetic diatance of IR4 also showed that there existed mixed subgroup and invasion between YN and OY.Three types of IR4 experienced two differentiations and two separations.
Analysis of sequence showed that the terminal untrantion regions(UTR) of genome of RSV had hight conservation,with variation between YN an OY. The UTR could form stable hairpin structure.Analysis of amino acid sequence showed that RdRp had transmembrane segments, coiled coils and some protein functional sites such as short-chain dehydrogenases/reductases family signature.NS2 had a strong potential cleavage site of signal peptide.NSvc2 had an N-signal peptide, a strong potential cleavage site of signal peptide and the property of membrane protein. NS3 had a coiled coil, some protein functional sites, and a differences of C-terminal hydrophobicity between YN and OY.CP had a coiled coil and some protein functional sites. SP and NSvc4 both had a potential cleavage site of signal peptide,a transmembrane segment and somes protein functional sites.Analysis of stop codons indicated that RSV prefers to use UAG as the stop codon and there are differences on preference of stop codon between YN and OY. Analysis of sequence showed that IR2-4 had direct repeat fragments and inverted repeat fragments, those could formed stable hairpin structure. IR3 and IR4 even had obvious insert and missing sequences.
A recombinant RNA of one isolate of Rice stripe virus(RSV) from Chuxiong(YCX07), Yunnan province, China, was sequenced. The RNA(YCX07R) was recombined from the 3' segments of RNA2 and RNA3 of RSV. The recombinant RNA uses ambisense coding strategy and encodes two proteins, namely YCX07R-5P and YCX07R-3P. The two proteins located on the 5' end of the plus and minus strand, respectively. This is similar to the four RNAs of RSV. It was discussed that the RNA was recombined from abortion replication or linked by two recombinant fragments through the recombinant site directly.
引文
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