水稻黑条矮缩病毒江苏玉米分离物全基因组序列及进化分析

 利用RT-PCR从江苏玉米上克隆水稻黑条矮缩病毒(RBSDV)的全基因组,其基因组10个片段核苷酸数目和蛋白编码情况与已报道的RBSDV分离物基本一致。 基因组的序列一致性分析和系统进化树表明,RBSDV基因组片段间存在频繁的RNA重排现象;江苏玉米分离物(JS)与湖北玉米分离物(HuB)和河北小麦分离物(HeB)的整体亲缘关系较近,而与安徽分离物(AH-MX8)的整体亲缘关系最远。综合本研究及前人对S8 和S10的研究,RBSDV基因组不同片段的进化中RNA重组的作用不同: S1、S2和S4中没有RNA重组;S3、S5、S6、S8和S10中存在低频率重组;S7 和S9存在较高频率重组,其中S7的高频率重组尤为显著。     

黄瓜绿斑驳花叶病毒安徽分离物全基因组序列测定及分析

通过胶体金免疫层析试纸条和RT-PCR等手段对采自安徽和县的西瓜病株进行检测,确定其病原为黄瓜绿斑驳花叶病毒(Cucumber green mottle mosaic virus,CGMMV)。为明确CGMMV安徽分离物CGMMV-Anhui的分类地位,进一步克隆了该病毒的全基因组序列,分析了其基因组结构特征。结果表明,CGMMV-Anhui基因组全长为6 423bp(GenBank登录号KT236095),与已报道的CGMMV的编码区的基因结构一致,仅5′和3′端非编码区核苷酸数目略有差异。将CGMMV-Anhui与已报道的分离物的全基因组序列和外壳蛋白基因序列进行系统发育分析,显示CGMMV不同分离物可分为亚洲和欧洲两个组,安徽分离物CGMMV-Anhui与亚洲分离物亲缘关系较近,可能具有共同的侵染源。     

水蜡A病毒在呼和浩特市和哈尔滨市紫丁香上的发生及其基因组分子特征分析

为明确侵染紫丁香Syringa oblata并引起褪绿花叶症状的病毒种类及其基因组分子特征,利用透射电子显微镜对分离自呼和浩特市和哈尔滨市的紫丁香病样中的病毒粒子进行观察,并通过小RNA高通量测序和RT-PCR技术对其进行检测分析。结果表明,在紫丁香显症叶片的病毒粗提液中观察到长约600 nm、宽约13 nm的线状病毒粒子。利用小RNA高通量测序和RT-PCR技术从病样中检测到水蜡A病毒（Ligustrum virus A,LVA）,发病率为3.7%。呼和浩特市紫丁香分离物LVA-Sob的基因组序列全长8 525 nt,包含6个开放阅读框,分别编码Rep（1 968 aa）、TGB1（229 aa）、TGB2（107 aa）、TGB3（60 aa）、CP（294 aa）和NABP（119 aa）共6个蛋白。序列一致性分析表明,分离物LVA-Sob与韩国水蜡树分离物LVA-SK的基因组序列一致率高达97.9%,而与我国辽宁省暴马丁香分离物LVA-DX的基因组序列一致率仅为73.6%。在这3个LVA分离物基因组中没有检测到重组事件;基于基因组和cp基因序列的系统发育树显示这3个LVA分离物形成一个分支,并与瑞香S病毒（daphne virus S,DVS）有较近的亲缘关系。     

甜瓜黄斑病毒在海南黄瓜上的发生分布及序列分析

 应用特异性引物MYSV-L-F和MYSV-L-R对海南5个市县采集的150份疑似感染病毒病的黄瓜样品进行RT-PCR检测,在三亚、乐东和东方等3个市县的18份样品中检测到甜瓜黄斑病毒(Melon yellow spot virus, MYSV)。选取采自三亚的分离物C29(MYSV-Hainan)进行MYSV全基因组克隆及序列分析,结果表明:该分离物的L RNA、M RNA和S RNA基因组全长分别为8 918 nt、4 815 nt和3 257 nt,与已知MYSV分离物的核苷酸相似性分别为97.4%~97.7%、96.2%~97.9%和94.8%~99.8%,系统进化关系分析与相似性分析一致,序列相似值越高,系统进化关系越近。     

甜瓜黄斑病毒在海南黄瓜上的发生分布及序列分析

 应用特异性引物MYSV-L-F和MYSV-L-R对海南5个市县采集的150份疑似感染病毒病的黄瓜样品进行RT-PCR检测,在三亚、乐东和东方等3个市县的18份样品中检测到甜瓜黄斑病毒(Melon yellow spot virus, MYSV)。选取采自三亚的分离物C29(MYSV-Hainan)进行MYSV全基因组克隆及序列分析,结果表明:该分离物的L RNA、M RNA和S RNA基因组全长分别为8 918 nt、4 815 nt和3 257 nt,与已知MYSV分离物的核苷酸相似性分别为97.4%~97.7%、96.2%~97.9%和94.8%~99.8%,系统进化关系分析与相似性分析一致,序列相似值越高,系统进化关系越近。     

黄瓜绿斑驳病毒河北分离物基因组克隆及序列分析

为揭示河北省黄瓜绿斑驳病毒(Cucumber green mottle mosaic virus,CGMMV)分类地位及系统进化情况,通过分子克隆测定了来自河北省西瓜产区分离获得的分离物CGMMV-chb的近全基因组序列,分析其基因组结构特征;并依据近全基因组核苷酸序列及外壳蛋白氨基酸序列进行了系统进化关系分析。结果表明,CGMMV-chb近全基因组大小为6 383 nts,Gen Bank登录号为KJ658958,含4个开放阅读框,编码4种蛋白;与Gen Bank库中的其它12个CGMMV分离物的核苷酸相似性为92%~100%,氨基酸相似性为98%~100%。CGMMV-chb与韩国分离物CGMMV-KW基因序列相似性最高,为98%~100%,与以色列分离物CGMMV isolate Ec基因序列相似性最低,为92%~99%;系统进化关系中CGMMV-chb与其它中国分离物、日韩分离物亲缘关系较近,处于同一亚组的不同分支中,与以色列分离物亲缘关系相对较远。     

黄瓜绿斑驳花叶病毒山西西瓜分离物外壳蛋白基因序列分析

通过病毒dsRNA分离技术、非序列依赖性PCR扩增(sequence-independent amplification,SIA)技术和RTPCR等手段对采自山西太谷的西瓜病样进行了检测与鉴定,确定其为黄瓜绿斑驳花叶病毒(Cucumber green mottle mosaic virus,CGMMV)所侵染。为明确CGMMV西瓜分离物(CGMMV-SXTG)的分类地位,本研究进一步克隆了CGMMV-SXTG的外壳蛋白基因(coat protein,CP)全序列并进行序列分析,系统进化树分析显示该分离物与亚洲分离物亲缘关系较近,而与欧洲分离物亲缘关系较远,表明该病毒的不同分离物在分组上可能与地域有一定的关系;接着对不同分离物的CP基因核苷酸序列和氨基酸序列进行同源性比对分析,结果表明该分离物与中国山东分离物(TANG)同源性最高,分别达到99.8%和99.6%。     

北京地区番茄黄化曲叶病病毒分离物测定及株系的初步鉴定

 番茄黄化曲叶病毒病是番茄生产中的一种毁灭性病毒病害,2009年传入北京。利用烟粉虱传双生病毒简并引物PA/PB对2010年~2011年采集自北京市5个区县的53个番茄样品进行检测,30个表现典型黄化曲叶病症状的样品均扩增得到约500 bp的特异条带,测定了其中7个样品的部分序列,经序列比对分析表明其为番茄黄化曲叶病毒（Tomato yellow leaf curl virus, TYLCV）。利用TYLCV特异引物TJ-F/TJ-R、TY-F/TY-R对样品BJDXXY、BJFS02、BJFS03、BJMY2231进行TYLCV基因组克隆和序列测定,经分析4个样品携带的TYLCV基因组长度均为2 781碱基,编码6个蛋白。基因组序列比较发现,这4个分离物与TYLCV-Israel株系同源性达到98%以上;通过建立系统发育树,发现BJDXXY、BJFS02、BJFS03与河北分离物（HBLF4）、山东分离物（SDSG）亲缘关系较近,BJMY2231与上海分离物（TYLCV-Israel）、江苏分离物（JSNJ1）亲缘关系较近。     

侵染梨的苹果茎痘病毒基因组序列及小RNA分析

苹果茎痘病毒(Apple stem pitting virus,ASPV)是危害梨(Pyrus spp.)和苹果(Malus spp.)的重要病毒。本研究采用小RNA深度测序技术获得了ASPV基因组的部分序列,在此基础上设计引物对该病毒基因组进行RT-PCR扩增,通过序列拼接得到1个来源于玉露香(Yuluxiang)梨的ASPV分离物(YLX)长度为9 291个核苷酸(nt)(不包括基因组5'末端约30个核苷酸)的基因组序列,该序列与已报道的13个ASPV分离物的基因组核苷酸序列相似性为71.6%~80.7%,与多个来自苹果的ASPV分离物系统进化关系较近。首次分析了来源于ASPV基因组的干扰性小RNA(siRNA),发现来源于ASPV基因组链和互补链的siRNA长度均以21 nt和22 nt为主,siRNA的5'端具有一定的碱基偏好性。本研究结果为深入了解ASPV的分子特性提供了重要信息。     

北京地区茄子感染番茄褪绿病毒的分子鉴定

为明确北京地区茄子感染番茄褪绿病毒(Tomato chlorosis virus,To CV)的情况,于2015年3—6月收集了10份疑似感染To CV的设施茄子样品,通过PCR分子鉴定法进行检测,并进一步对扩增阳性样品To CV的CP基因采用邻接法进行了系统进化分析。结果表明,10个检测样品中有4个扩增得到约463 bp的特异条带,经测序与Gen Bank中To CV序列相似性达到99.0%以上,表明这4个样品均携带有该病毒,检出率为40%;To CV茄子分离物的CP基因序列大小为774 bp,Gen Bank登录号为KT751008,与To CV北京番茄分离物(KC311375)同源性最高,达到99.9%,确认该序列为To CV片段;系统进化树显示,To CV茄子分离物与To CV日本分离物(AB513443)处于同一分支,具有密切的亲缘关系,表明不同国家To CV分离物之间的亲缘关系与地理距离具有一定的相关性。     

黑龙江地区番茄斑萎病毒的鉴定及其部分生物学特征分析

近年来,番茄斑萎病毒Tomato spotted wilt tospovirus (TSWV)在我国多个地区发生严重危害。本研究采用小RNA深度测序和RT-PCR相结合的方法对采自黑龙江的番茄病毒病样品中的病毒进行了鉴定。提取番茄样品的RNA并构建小RNA文库进行测序,数据分析发现比对至TSWV基因组的reads数占比对到病毒核酸总reads数的92.64%,表明侵染此番茄样品的病原物可能是TSWV。利用RT-PCR方法进一步确定侵染此番茄样品的病毒为TSWV,将其命名为TSWV-HLJ1。对TSWV-HLJ1的核苷酸序列进行分析并构建系统进化树,结果表明TSWV-HLJ1与TSWV云南甜椒分离物(TSWV-YNgp)的亲缘关系最近。介体传毒试验表明,西花蓟马可将TSWV-HLJ1传播感染健康寄主植物。摩擦接种试验表明,TSWV黑龙江分离物能够侵染本氏烟、辣椒和番茄。这是我国首次报道在黑龙江地区发现TSWV的危害。     

Tomato Spotted Wilt Tospovirus Adapts to the TSWV N Gene-Derived Resistance by Genome Reassortment

ABSTRACT Pathogen- and host-derived resistance have been shown to suppress infection by many plant viruses. Tomato spotted wilt tospovirus (TSWV) is among these systems; however, it has easily overcome nearly all host resistance genes and has recently been shown to overcome resistance mediated by the TSWV N gene. To better understand the resistance-breaking mechanisms, we have chosen TSWV N gene-derived resistance (TNDR) as a model to study how plant viruses defeat resistance genes. A defined viral population of isolates TSWV-D and TSWV-10, both suppressed by TNDR, was subjected to TNDR selection by serial passage in an N-gene transgenic plant. The genotype analysis demonstrated that the mixed viral population was driven to form a specific reassortant, L(10)M(10)S(D), in the presence of TNDR selection, but remained as a heterogeneous mixture in the absence of the selection. A genotype assay of 120 local lesion isolates from the first, fourth, and seventh transfers confirmed the shift of genomic composition. Further analysis demonstrated that the individual L(10), M(10), and S(D) RNA segments were each selected independently in response to TNDR selection rather than to a mutation or recombination event. Following the seventh transfer on the N-gene transgenic plants, TSWV S RNA remained essentially identical to the S RNA from TSWV-D, indicating that no intermolecular recombination occurred between the two S RNAs from TSWV-10 and TSWV-D nor with the transferred N gene. These results support the hypothesis that TSWV utilizes genome reassortment to adapt to new host genotypes rapidly and that elements from two or more segments of the genome are involved in suppression of the resistance reaction.     

Occurrence and diversity of Tomato spotted wilt virus isolates breaking the Tsw resistance gene of Capsicum chinense in Yunnan,southwest China

Widely used resistant peppers (Capsicum spp.) bearing the Tsw locus triggered the rapid emergence of resistance‐breaking (RB) isolates of Tomato spotted wilt virus (TSWV) around the world. However, although TSWV‐induced diseases have rapidly increased in Yunnan, southwest China, in recent years, no information is available about the diversity of TSWV isolates in this region. In this study, the occurrence of natural TSWV RB variants among isolates collected in Yunnan is reported. Initially, a TSWV isolate from asparagus lettuce (TSWV‐LE) was collected in Yunnan in 2012. Surprisingly, this isolate of TSWV induced systemic necrosis on pepper carrying the Tsw resistance gene. Novel TSWV isolates, collected in 2015, included a tomato isolate (TSWV‐YN18) and a tobacco isolate (TSWV‐YN53) that also overcame Tsw‐mediated resistance. TSWV‐YN18 induced systemic ringspots, whereas TSWV‐YN53 caused systemic chlorotic mottling. Variations in the TSWV nonstructural (NSs) protein are the key determinants associated with Tsw resistance‐breaking isolates. It was found that TSWV‐LE NSs retained the hypersensitive response (HR) induction, whereas TSWV‐YN18 and TSWV‐YN53 NSs were unable to induce HR. However, the NSs of all three RB isolates suppressed RNA silencing. Sequence analysis of the NSs revealed that RB isolates of Yunnan have no amino acid mutation sites common to other previously reported RB isolates. However, two amino acids (F74 and K272) on TSWV‐LE NSs make it distinct from TSWV‐YN18 and TSWV‐YN53. The occurrence of different RB isolates and the failure of Tsw‐mediated resistance control pose serious threats to domestic pepper crops in southwest China.     

红花黄萎病病原菌鉴定

番茄斑萎病毒Tomato spotted wilt virus （TSWV）是我国进境植物检疫性有害生物,近年来相继在国内一些省份发现。利用 TSWV 的通用引物 NF302／NR575对从山东烟台地区收集的15份疑似感染番茄斑萎病毒病的番茄样品进行检测;进一步对特异引物 TSWV-NF2037／TSWV-NR2825扩增的 TSWV 的 N 基因序列克隆、测序,并对 N 基因片段编码氨基酸进行遗传距离及系统发育分析。结果表明,15份疑似样品中有4个样品扩增得到 TSWV 病毒片段;基于 N 基因序列分析发现,山东 TSWV 番茄分离物与云南 TSWV 番茄分离物（AEI70836．1）的遗传距离最近,为0．8％,且与云南 TSWV 番茄分离物聚为一支。这是山东地区首次利用分子标记证实番茄斑萎病毒病的危害。     

Impeded Thrips Transmission of Defective Tomato spotted wilt virus Isolates

Two defective RNA-containing isolates (Pe-1 and 16-2) and an envelope-deficient (env ) isolate of Tomato spotted wilt virus (TSWV) were tested for their transmissibility by Frankliniella occidentalis. The Pe-1 isolate contained a truncated L RNA segment that barely interfered with symptom expression and replication of the wild-type (wt) L RNA segment. This isolate was transmitted with an efficiency of 51%, a value comparable to that found for wt TSWV (54%). Isolate 16-2, which contained a genuine defective interfering L RNA as concluded from its ability to suppress wt L RNA synthesis and attenuation of symptom expression, was not transmitted at all. The midguts of all larvae that ingested Pe-1 became infected, whereas limited midgut infections were found in 24% of the larvae that ingested 16-2. This difference in infection could be explained by the presence of a low number of infectious units in the inoculum ingested from plants as demonstrated in infection experiments and verified by northern blot analysis. The env isolate failed to infect the midgut after ingestion and could not be transmitted by any thrips stage. This isolate also cannot infect primary thrips cell cultures. Taken together, these results suggest that the envelope of TSWV contains the determinants required for binding and subsequent infection of thrips cells.     

The S RNA segment determines symptom differences on Tetragonia expansa between two Watermelon silver mottle virus isolates

The WS-Y isolate of Watermelon silver mottle virus (WSMoV) causes severe necrosis in Tetragonia expansa. To determine the RNA segment that induces symptoms, genome reassorants between WS-Y and an isolate causing mild mottle, WS-O, were generated. The origin of each segment in the reassortants was identified by RT-PCR and subsequent restriction enzyme analysis of the amplified fragments. Thirty genome reassortants were isolated from co-infected T. expansa plants. The reassortants with the S RNA segment of WS-Y caused severe necrosis, while those with the S RNA segment of WS-O caused a mild mottle; hence, the S RNA determined symptom expression. The incidence of reassortants was disproportional among genotypes. The most frequent genome reassortant possesses the L RNA of WS-Y, the M RNA of WS-O and the S RNA of WS-Y. A similar ratio of genotypes was found in isolates of local lesions on Chenopodium quinoa. These results strongly suggested that competition occurred independently between the individual RNA segments in a co-infected T. expansa plant, not between isolates.     

Characterization of a vector-non-transmissible isolate of Tomato spotted wilt virus

The characteristics of a thrips‐non‐transmissible isolate of Tomato spotted wilt virus (TSWV), designated TSWV‐M, were compared with those of a thrips‐transmissible isolate, designated TSWV‐T. TSWV‐M showed a narrower host range than TSWV‐T. Adult thrips failed to transmit TSWV‐M, although the vector acquired the virus during the larval stages. TSWV‐M was detected by RT‐PCR in adult thrips bodies, but not in thrips heads, suggesting that loss of thrips transmissibility was the result of the absence of virus in adult thrips salivary glands. Whereas N (nucleoprotein), NSs (non‐structural protein) and G_C (the C‐terminal portion of the glycoprotein precursor protein) were present in similar amounts in leaf tissue from TSWV‐M‐ or TSWV‐T‐infected plants, G_N (the N‐terminal portion of the glycoprotein precursor protein) was present at much lower amounts in TSWV‐M‐ than in TSWV‐T‐infected plants. SDS‐PAGE and immunoblotting analysis of TSWV‐M and TSWV‐T virion preparations with G_N‐ and G_C‐specific antibodies revealed similar amounts of the G_N and G_C glycoproteins in TSWV‐T virions, but lower amounts of G_N than G_C in TSWV‐M virions. This resulted in a statistically significant reduction in the G_N/G_C ratio in TSWV‐M virions. In affinoblots, the G_C and G_N glycoproteins of TSWV‐M exhibited weak binding with lectins showing affinity for N‐linked oligosaccharide structures. Sequence analysis of M RNA (medium segment of the TSMV genome) revealed no deletions or frameshift mutations in the G_N/G_C precursor of TSWV‐M. However, five amino acid changes were detected in the G_N/G_C precursor. A single, relatively conservative amino acid substitution (V→I) was observed in the NSm protein. Sequence analysis of S RNA (small portion of the TSMV genome) revealed a large intergenic region with no changes in the N protein and with three amino acid changes in the NSs protein.     

Effects of Temperature and Host on the Generation of Tomato Spotted Wilt Virus Defective Interfering RNAs

ABSTRACT The generation of defective interfering (DI) RNA molecules of tomato spotted wilt tospovirus (TSWV) was studied by serially passaging in-ocula from plant to plant under different controlled conditions. DI RNAs were generated at higher rates in plants at 16 degrees C than in plants incubated at higher temperatures. Another factor promoting the TSWV DI RNA generation was the use of high virus concentrations in the inocula. The solanaceous species Capsicum annuum, Datura stramonium, Lycopersicon esculentum, Nicotiana benthamiana, and N. rustica supported the generation of DI RNAs, whereas the virus recovered from the inoculated composite species, Emilia sonchifolia, remained free of any DI RNA under all conditions tested. This study resulted in a strategy to maintain DI RNA-free TSWV isolates, as well as in an efficient way to produce a large population of different DI RNA species. A single DI RNA species usually became dominant in an isolate after a few rounds of serial inoculations. The possible mechanisms involved in TSWV DI RNA generation under different inoculation circumstances are discussed.     

蚕豆萎蔫病毒2号安徽分离物全基因组序列测定与分析

利用酶联免疫和RT-PCR技术对采自安徽地区的蚕豆病株进行检测,确定其病原为蚕豆萎蔫病毒2号Broad bean wilt virus 2(BBWV2)。为明确BBWV2安徽分离物(BBWV2-AH)的分类地位,克隆了该分离物的全基因组序列,分析了其基因组特征。结果表明,BBWV2-AH RNA1全长为5 944 bp(GenBank登录号:KY606992),含有1个ORF;BBWV2-AH RNA2全长3 587bp(GenBank登录号:KY606993),含有1个ORF。全序列核苷酸和氨基酸相似性分析显示,BBWV2-AH RNA1与BBWV2其他分离物的核苷酸、氨基酸相似性分别为78.4%~96%和87.1%~99%;BBWV2-AH RNA2与BBWV2其他分离物的核苷酸、氨基酸相似性分别为76.8%~95.5%和88.2%~98.3%。全基因组核苷酸序列系统发育分析显示,BBWV2-AH RNA1与中国的BBWV2-Hunan RNA1的亲缘关系最近,而BBWV2-AH RNA2与韩国的多个分离物聚集在一起,再与中国的分离物BBWV2-B935形成一个分支。