应用PCR-SSCP技术快速检测我国水稻条纹病毒的分子变异

应用PCR SSCP技术快速检测我国水稻条纹病毒病害特异性蛋白 (SP)基因和外壳蛋白 (CP)基因的分子变异。结果发现我国水稻条纹病毒 7个分离物之间存在广泛的变异 ,其中 ,PJ分离物的SP基因和JD分离物的CP基因不能扩增出来 ,能扩增出的 6个分离物的CP基因变性电泳后带型各不相同 ,但SP基固表现出 5种带型 ,其中云南省的YL和BS分离物带型一样。     

应用PDR—SSCP技术快速检测我国水稻条纹病毒的分子变异

应用PCR－SSCP技术快速检测我国水稻条纹病毒病害特异性蛋白（SP）基因和外壳蛋白（CP）基因的分子变异。结果发现我国水稻条纹病毒7个分离物之间存在广泛的变异,其中,PJ分离物的SP基因和JD分离物的CP基因不能扩增出来,能扩增出的6个分离物的CP基因变性电泳后带各不相同,但SP基因表现出5种带型,其中云南省的YL和BS分离物带型一样。     

水稻条纹病毒两个分离物RNA4基因间隔区的序列比较

通过RT-PCR扩增了我国水稻条纹病毒(RSV)山东济宁(JN)、云南宜良(YL)两个分离物RNA4基因间隔区(intergenic region,IR)序列,并克隆于pGEM-T easy载体上.序列分析结果表明:JN、YL两分离物RNA4 IR均由654个核苷酸组成,两者之间的同源率为92%.JN、YL两个分离物RNA4 IR在AU碱基富集处可形成两个明显的发夹结构,其中一个序列比较保守,形成的发夹结构稳定;但另一个由于碱基变异导致所形成的发夹结构的稳定性在各个分离物中差异较大.这些结果说明了我国水稻条纹病毒存在明显的分子变异.     

韭葱黄条病毒、洋葱黄矮病毒和胡葱黄条病毒六安分离物CP基因克隆及同源性分析

设计特异性引物PCR扩增了六安大蒜病样中的韭葱黄条病毒(Leek yellow stripe virus,LYSV)、洋葱黄矮病毒(Onion yellow dwarf virus,OYDV)和胡葱黄条病毒(Shallot yellow stripe virus,SYSV)的全长CP基因,插入到pGEM-T载体并测序。分别比较3种病毒CP基因种内变异性和种间亲缘关系。结果表明LYSV六安分离物CP基因由864个碱基组成,与Genbank上已报道的68个LYSV不同分离物CP基因的核苷酸序列同源性为76.12%～84.31%;OYDV的CP基因由771个碱基组成,与Genbank上已报道的86个OYDV不同分离物同源性为81.06%～90.40%;SYSV的CP基因由774个碱基组成,与Genbank上已报道的11个SYSV不同分离物CP基因同源性为88.63%～94.32%;从分析结果来看,LYSV的CP基因不同分离物之间变异性较大,OYDV CP变异性不大,SYSV变异性很小;3种病毒都有1个以上的宿主,病毒种内不同宿主分离物之间CP序列差异很小。进化分析显示OYDV和SYSV的CP基因亲缘性较近并成簇,LYSV的CP基因与OYDV和LYSV的CP基因亲缘性较远。     

CP gene cloning and sequence analysis of Liu'an isolates of Leek yellow stripe virus, Onion yellow dwarf virus and Shallot yellow stripe virus

设计特异性引物PCR扩增了六安大蒜病样中的韭葱黄条病毒(Leek yellow stripe virus,LYSV)、洋葱黄矮病毒(Onion yellow dwarf virus,OYDV)和胡葱黄条病毒(Shallot yellow stripe virus,SYSV)的全长CP基因,插入到pGEM-T载体并测序.分别比较3种病毒CP基因种内变异性和种间亲缘关系.结果表明LYSV六安分离物CP基因由864个碱基组成,与Genbank上已报道的68个LYSV不同分离物CP基因的核苷酸序列同源性为76.12%～84.31%;OYDV的CP基因由771个碱基组成,与Genbank上已报道的86个OYDV不同分离物同源性为81.06%～90.40%;SYSV的CP基因由774个碱基组成,与Genbank上已报道的11个SYSV不同分离物CP基因同源性为88.63%～94.32%;从分析结果来看,LYSV的CP基因不同分离物之间变异性较大,OYDV CP变异性不大,SYSV变异性很小;3种病毒都有1个以上的宿主,病毒种内不同宿主分离物之间CP序列差异很小.进化分析显示OYDV和SYSV的CP基因亲缘性较近并成簇,LYSV的CP基因与OYDV和LYSV的CP基因亲缘性较远.     

悬浮细胞再生表达外壳蛋白的转基因Indica水稻对水稻条纹病毒的抗病性(英文)

合成、克隆了水稻条纹病毒中国株的外壳蛋白基因并进行了序列分析,由Indica水稻成熟胚的愈伤组织形成胚性运浮细胞。用含有CP基因的pROK2表达载体的DNA包被1.09μm直径钨粉颗粒轰击培养细胞。被轰击的培养物在含有G418（40mg／mL,）的培养基中进行选择培养,由对G418抵抗的愈伤组织中获得10株再生株。用32P－dCTP标记的CP基因作为探针,以Southernblot测定其转化特性。由抗病的和对照的植株抽提基因组DNA用EcoRI和BamHI进行酶切,其中两个植株显示出0.6kh和0.7kb两条条交带．其大小与CP基因相对应。Westernblot和ELISA测定进步证明CP（32kDa）在转基因水稻中表达。16株转基因植株和100株对照植株用带毒的叶蝉接种,接种病毒后24d只有37.5％的CP转基因植株产生病毒症状,而对照植株为96％。进一步证明转基因水稻植株具有对RSV的抗病性。转基因植株T1代CP的表达分离比例为3.6:1。     

水稻条纹病毒RNA4基因间隔区的分子变异

应用反转录－聚合酶链式反应（RT－PCR）和单链构象多态性（single-strand conformation polymorphism,SSCP)技术快速检测我国水稻条纹病毒（RSV）RNA4基因间隔区（intergenic region,IR)的分子变异,结果表明,我国RSV RNA4 IR存在分子变异。供试的7个分离物共有4种泳动带型,其中YL、BS、JD、LY分离物完全一致,而YL、BS、YL及JD4个分离物序列完全一致;JN、PJ、SQ3个分离各不一样,序列之间的同源性均在92％－94％之间.IR序列内部具有两个重要的结构特征：（1）有两处反向重复序列,可形成两个明显的发夹结构,其中一个序列比较保守,形成的发夹结构稳定;但中一个发夹结构由于碱基变异导致其稳定性在各个分离物中差异较大;（2）具有插入序列,相对于日本M分离物,我国7个分离物都有一段长19bp的插入序列,这段插入序列比较保守,各分离物之间仅有1－2个碱基的差异。     

吡虫啉对水稻体内条纹病毒的胁迫效应

水稻条纹叶枯病为灰飞虱(SBPH)传播的一种病毒病,前些年在长江流域尤其江苏地区暴发成灾.为探讨杀虫剂吡虫啉对水稻体内条纹病毒(rice stripe virus,RSV)的胁迫效应,本研究模拟大面积生产上的用药方式,在灰飞虱传毒48 h后对稻苗分别施药1、2、3和4次(以B₁、B₂、B₃和B₄表示),以实时荧光定量PCR(real-time PCR)和蛋白免疫印痕(Western blotting, WB)等方法对稻苗中RSV NS3、CP、SP、NSvc4等4种基因的表达和CP、SP两种蛋白的含量进行分期检测.结果表明: 1)吡虫啉影响4种基因的表达,且其影响程度与施药强度及基因类型有关:有3个处理NS3基因表达水平上调,其中施药4次、接虫后16 d\[以(B₄, 16 d)表示,下同\]的表达水平最高,达10.86,其他处理的NS3基因表达都明显受到抑制.几乎所有B₂和B₃处理都使CP、SP和NSvc4基因的表达受到明显抑制,其相对表达水平为0～0.74;而B₁和B₄的一半处理明显促进其上调,其中(B₁, 16 d)和(B₄, 16 d)SP基因的表达量最高,分别为258.89和730.54.2)吡虫啉对CP、SP基因和CP、SP蛋白表达模式的胁迫效应不同,如(B₁, 19 d)CP基因几乎没有表达(0),但其相应的CP蛋白却明显上调(23.08)
.
     

侵染新疆甜瓜的黄瓜花叶病毒衣壳蛋白的克隆及其序列分析

利用同源克隆的方法,扩增获得了新疆16个地区CMV病毒分离物CP蛋白基因全长序列,16个地区CMV病毒分离物CP蛋白基因全长约1 100 bp,最大开放阅读框介于630~690 bp,编码约210个氨基酸,蛋白质大小约25 k D。序列比对发现16个地区CMV病毒核酸序列的3'末端非编码区保守性较低,编码区及其5'端序列保守性较高,氨基酸序列的两端均存在不同数量的变异位点,根据CMV病毒同源性比对结果,16个地区病毒均属于同一CMV亚组。通过核酸序列构建的分子进化树分析发现,本研究分离获得的新疆16个地区CMV病毒衣壳蛋白基因序列则存在较高同源性且不同地区病毒分离物间相对遗传距离差异较小,16个地区与国内外15个地区病毒分离物相比均存在较大差异,统计分析显示,新疆CMV分离物组内核酸序列相对遗传距离差异不显著,相比参考序列,其差异则极显著,这一结果与聚类分析结果能够得到相互印证。分析认为,不同地区CMV病毒CP蛋白基因虽然与外来地区病毒基因存在较大差异,但由于本研究分离的新疆16个地区CMV病毒衣壳蛋白基因序列存在较高同源性且病毒因受不同理化条件的影响往往存在不同程度的变异率,因此认为,分离获得的新疆16个地区CMV病毒可能受地理位置、气候等因素的影响,其基因组中存在异于其他地区不同程度的变异趋势与类型,导致相应蛋白质稳定性也随之发生变化,从而更好的适应在新疆甜瓜植株上的侵染和定殖。     

侵染菊花的番茄不孕病毒的鉴定及其外壳蛋白基因的克隆

从菊花花叶病标样中分离到一球形病毒分离物,直径25～29 nm,与TAV抗血清反应呈阳性.根据英国报道的番茄不孕病毒(TAV-En)CP基因序列,设计合成一对引物,对该病毒RNA进行RT-PCR扩增,得到与预期大小相符的特异扩增带.将其克隆到pGEM-T easy中,经酶切和序列分析表明所克隆的是TAV CP基因,与已知的6个株系相应序列同源性均在96.4%以上.     

Nucleotide Sequence Assessment of Four ORFs of Citrus Tristeza Virus: Evidence of Recombination

Citrus Tristeza Virus (CTV), usually occurs in nature as a mixture of genotypes. Six naturally infected citrus (Citrus sinensis) trees grafted on sour orange rootstock were collected from three citrus growing governorates in Egypt (Sharqia, Qalyubia and Garbia). In this study, RT-PCR, Single-Strand Conformation Polymorphism (SSCP) and nucleotide sequence analysis were used for four independent CTV genomic regions (p65, p18, p20, and p23) to detect and assess the sequence and genetic variabilities among CTV Egyptian isolates. RTPCR products (650 bp) for the CTV p23 gene obtained from the selected isolates were used for the SSCP analysis and DNA sequencing. SSCP patterns of p23 gene for individual isolates yielded different complex haplotype patterns. Nucleotide sequence analysis of p23 region amplified from six isolates under study revealed that p23 shared high nucleotide identity 98.7% with T36 isolate from USA, Florida. Phylogenetic analysis of p23 gene indicated a close evolutionary relationship between all examined isolates and Qaha isolate (T36 isolate group), suggesting that they may have originated from closely related ancestors. Nucleotide sequence analysis of the three genes located on CTV 3′-coterminal overhang, p18, p20 and p65, amplified from isolate A3, Sharqia governorate, revealed that the p18, p65, and p20 genes were related to the T3-KB isolate from South Africa with 99%–100% sequence homology. Phylogenetic relationship analysis for p65, p18 and p20 ORFs clustered the current A3 isolate with T3 genotype group. The recombination analysis identified three of six isolates from Sharqia, and Garbia as potential recombinant for p23 gene. The isolates T36 and T3 were identified as major donors for recombination events in isolate A3. Our results concluded that p23 ORF likely to be as a hotspot region for recombination and originated through recombination event. The current study indicated that recombination is an important factor for the origin of CTV strains in Egypt.     

Molecular Characterization of Jordanian Isolates of Cucurbit yellow stunting disorder virus

Cucurbit yellow stunting disorder virus (CYSDV) causes high yield losses to cucurbits in many parts of the world. In 1995, it was detected for the first time in Jordan but Jordanian isolates have never been characterized at the molecular level. In 2005 and 2006, leaf samples (2344) from symptomatic plants were collected from Jordan Valley, Ma'daba, Al‐Mafraq, Al‐Karak, Jarash, Al‐Tafila, Al‐Balqa’, Al‐Zarqa’, Amman and Irbid. Detection by tissue blot immunoassay (TBIA) showed that the infection rate of CYSDV in collected samples was 58.5%. The coat protein (CP) gene of CYSDV was amplified from 36 selected samples by IC‐RT‐PCR. The amplicons (753 bp) from 16 isolates, representing all surveyed regions, were cloned and used for the single‐strand conformation polymorphism (SSCP) analysis. Seven different SSCP patterns (P1–P7) were observed for the analysed Jordanian isolates. For further characterization, the CP genes from isolates with different SSCP patterns were sequenced, and the sequences were deposited in the GenBank under the accession numbers DQ903105 – DQ903111 . Sequence alignment and phylogenetic analysis revealed that all CYSDV isolates investigated in this study were most closely related to isolates previously reported to belong to the Western group of CYSDV.     

Sequences of Tobacco Rattle Viruses from Potato

The RNA2 of the tobacco rattle virus (TRV) isolate 'Rostock' (TRV-R), and the coat protein gene (CP) of TRV isolate 'Mirow' (TRV-M) were sequenced. Both were isolated from potato. Sequence analysis revealed a 5' noncoding-region (NCR) and a CP gene, which are among the shortest of any tobravirus RNA2 sequenced so far. Downstream of the CP open reading frame (ORF) there was an ORF for a 8 k protein, that is probably a truncated 9 k protein, followed by an ORF for a 16 k protein and the 3' NCR. The 16 k protein and the 3' NCR showed a considerable sequence identity with the 3' end of TRV RNA1 and RNA2 from other TRV isolates. The high identity in the amino acid sequences of the CPs from TRV-R and TRV-M as well as other TRV isolates suggested that they are related to the TCM group of the genus Tobravirus and belong serologically to the RQ-serotype. This could be confirmed using a rabbit antiserum that was prepared against recombinant TRV-R CP expressed in bacteria. This serum was found to be suitable for differentiation of TRV-isolates.     

Differentiation of citrus tristeza closterovirus (CTV) isolates by single-strand conformation polymorphism analysis of the coat protein gene

Citrus tristeza closterovirus (CTV) isolates of several geographical origins were compared for variations in their coat protein (CP) gene by analysis of single-strand conformation polymorphism (SSCP). The CP gene of 17 isolates was reverse transcribed, amplified by polymerase chain reaction (PCR), and 22 clones were inserted into a plasmid vector. These clones were sequenced and found to have between 91.7% and 99.8% sequence homology. Clones were amplified and the PCR products denatured and compared by SSCP analysis in 8% polyacrylamide gels. Using two different electrophoretic conditions, the patterns were different for 16 or 17 clones. Four pairs of clones (T36/T66, P1/Q2, 03/8Q, and E1/E2) differing by 10, 2, 1 and 1 nucleotides, respectively, could not be distinguished using either condition. When these clones were compared by SSCP after digestion with Eco91I (BstEII) three of the pairs (T36/T66, P1/Q2, and 03/8Q) could be differentiated, whereas the clones E1 and E2 (differing by 1 nucleotide) remained indistinguishable. Thus, SSCP analysis combining two electrophoretic conditions and restriction of eight clones with Eco91I allowed discrimination between 21 of the 22 CP gene clones selected. SSCP analysis may provide a procedure to identify and differentiate CTV isolates based on comparisons of several genes or gene regions. It is rapid and cheap and may drastically reduce the amount of sequencing necessary for accurate comparisons.