我国部分苹果产区苹果锈果类病毒的检测和全序列分析

近年来,由苹果锈果类病毒Apple scar skin viroid(ASSVd)引起的苹果花脸病、锈果病在我国一些苹果产区日趋严重,对我国苹果生产和苹果产业发展造成严重危害。为了解ASSVd在我国一些苹果产区的发生和变异情况,采用RT-PCR对陕西、山东、山西、河北、北京和黑龙江6个苹果产区的35份苹果样品进行检测,并克隆获得30个分离物的基因组全序列,大小为330~333个核苷酸。分析表明,这些分离物的基因组全序列与GenBank中ASSVd基因组核苷酸序列相似度为96%~100%,在苹果锈果类病毒属的末端保守区及中央保守区保守,在致病区和左端区域有突变,一些分离物的突变位点相同。系统发育分析表明分离物因相同的突变位点而聚类,而与地理来源无关。     

侵染小苹果的苹果锈果类病毒的检测和全序列分析

小苹果是抗寒海棠类与大苹果的杂交后代,因耐寒能力强,口感好,被广泛用于嫁接与育种材料,是我国寒凉苹果产区宝贵的种质资源。苹果锈果类病毒(Apple scar skin viroid,ASSVd)侵染苹果后引起果实表面产生锈状斑、花脸、畸形等症状,严重降低果实品质和市场价值。2013年在调查苹果病毒病时发现北京市延庆县种植的小苹果表现出典型畸形症状,应用RT-PCR方法对其进行检测后经测序和序列分析表明,小苹果被苹果锈果类病毒侵染。克隆此分离物(ASSVd-YQ)全基因组序列,分析后得到其基因组全长为329个核苷酸,系统发育分析表明该分离物与来自不同国家和地区的ASSVd分离物间的进化关系极近。二级结构预测表明,该分离物的中央保守区与末端保守区与ASSVd参考序列相同。这是对侵染小苹果的ASSVd的首次检测和鉴定。     

烟台市富士苹果上苹果锈果类病毒分子变异分析

为明确苹果锈果类病毒(Apple scar skin viroid,ASSVd)在烟台市富士苹果上的变异情况,通过特异性引物对携带苹果锈果类病毒的富士嫩叶进行ASSVd全长扩增,利用生物学软件DNAMAN对所得变异序列进行分析并构建系统进化树。结果表明,从130个样品中筛选到36个阳性样品,36个阳性样品中共克隆获得52条329~333 nt的ASSVd变异序列,其中30个阳性样品含2条或2条以上的ASSVd序列。对所得变异序列进行序列比对发现,同一样品不同克隆间核苷酸序列相似性为94.0%~100.0%,所有变异序列核苷酸序列相似性为94.0%~99.7%,与Gen Bank中来自不同国家或地区的10条ASSVd分离物核苷酸序列相似性为88.3%~99.7%。将序列相似性低于97.0%的12条变异序列进行系统进化分析,结果显示除了333 nt变异序列ZS2-6与伊朗苹果分离物在同一分支外,其余11条变异序列位于同一分支。52条变异序列多序列比对发现,变异位点主要集中在TL区、P区和C区。研究表明烟台市富士苹果上ASSVd存在一定的分子变异。     

苹果锈果类病毒在八棱海棠种子中的分布及氢氧化钠脱毒效果分析

为明确苹果锈果类病毒在八棱海棠果实和种子中的分布特征、种传率以及药剂脱除效果,以带毒母株上的八棱海棠果实和种子为试材,运用RT-PCR技术分析了八棱海棠果实不同部位锈果类病毒的带毒率、实生后代的带毒情况以及氢氧化钠脱除病毒的效果。结果表明,八棱海棠果皮、果肉、种子以及种胚均不同程度携带苹果锈果类病毒,其带毒率分别为96.0%、96.0%、52.0%和4.0%;该病毒可经种子传递给后代,种传率为12.1%;经2%氢氧化钠溶液浸种10、15、20 min,种子的病毒检出率均为0,但后代实生苗的带毒率分别为2.5%、1.3%和0。表明苹果锈果类病毒可侵染种子不同部位并经种子传递给后代,氢氧化钠浸种是脱除该病毒的有效方法。     

苹果锈果类病毒(ASSVd)的种群及遗传变异分析

苹果锈果类病毒apple scar skin viroid(ASSVd)引起苹果锈果病,是限制我国苹果生产的重要因素之一。然而,目前对ASSVd全球种群的组成及遗传变异仍缺乏足够的了解。为此,本研究对GenBank中登录的212条基因组序列进行了比较、变异分析以及系统发育分析。确认ASSVd的种群符合准种模式,由165种序列相似但不相同的变体组成。以来自我国苹果的MW315909和MW302328为代表的两种变体的数量最多,是主流变体。依据参考序列(NC001340)分析碱基变异,发现碱基变异偏好于某种碱基,并且偏好于基因组上的一些特定位点。变异不仅发生在基因组二级结构的左末端区、致病区、中央区,也发生在可变区和右末端区。值得指出的是,基因组上有4个区域极少发生变异,为保守区。其中的两个保守区(末端保守区和中央保守区)是已知的,而在可变区与右末端区交界处的两个保守区是新发现的,它们对ASSVd的复制和移动可能具有重要作用。这些结果不仅有助于掌握ASSVd的发生及流行,而且为研发RT-PCR/qPCR检测技术提供了参考,为研究ASSVd与寄主的相互作用提供了线索。     

利用两种方法检测苹果锈果类病毒

以克隆ASSVd的部分序列,通过RT-PCR成功合成了地高辛标记的cDNA探针,提取苹果和梨树枝条的总RNA,用斑点杂交技术对其进行了检测试验,结果表明,探针具有很高的灵敏度和特异性。地高辛标记的cDNA探针不与阴性对照枝条RNA以及感染PBCVd、AFCVd、ADFVd枝条总RNA发生杂交,仅与感染ASSVd样品的总RNA杂交。     

北京平谷区苹果锈果类病毒检测初报

采集北京市平谷区‘中秋王’、‘寒富’苹果叶片样品共12份,以Northern杂交、RT-PCR方法检测苹果锈果类病毒(Apple scar skin viroid,ASSVd)带毒情况。结果表明,表现明显锈果症状的‘中秋王’样品均检出ASSVd,无明显症状的‘中秋王’样品没有检出ASSVd,而无明显症状的‘寒富’样品全部携带ASSVd。测序发现,所得序列与NCBI中已报道的ASSVd基因组序列相似性为91%~99%,且两品种中ASSVd主流序列完全相同。结果说明‘中秋王’对ASSVd较为敏感,感病后易于表现出明显的锈果症状;‘寒富’对ASSVd耐性较强,感病后不表现出明显症状。     

An important new apricot disease in Spain is associated with <Emphasis Type="Italic">Hop stunt viroid</Emphasis> infection

The province of Murcia (Murcia Region) is the one of the most important apricot growing regions in Europe. In recent years a fruit disorder named by growers as “degeneración” has been detected in apricot commercial orchards of this region, mainly in the variety Velázquez Fino. Affected fruits are characterized by changes in their external appearance involving rugosity and a loss of organoleptic characteristics, which leads to an unmarketable product. In order to identify the causal agent of this disorder, the presence of the most important viruses affecting stone fruit trees and Hop stunt viroid (HSVd) was tested. While negative results were obtained for all viruses analysed, the viroid was detected in all the symptomatic trees. Within a single tree, the viroid was restricted to branches bearing fruits with the characteristic symptoms but was usually absent from the rest of the tree. Sequence analysis of several isolates of HSVd obtained from these affected trees revealed the presence of two variants previously detected in other apricot cultivars. Taken together, these results suggest that degeneration is associated with HSVd.     

Characterization of a new viroid strain from hops: evidence for viroid speciation by isolation in different host species

A new viroid was detected in hops cultivated in Akita Prefecture, Japan where it is prevalent in many hops fields. In a survey of hop samples collected during the 1986–2002 growing seasons, the new viroid was present in the major Japanese hop-cultivating areas as early as the 1980s. A single-stranded circular RNA of 368–372 nucleotides that assume a highly basepaired, stable, rod-like secondary structure, shares 93%–98% sequence homology with Apple fruit crinkle viroid (AFCVd) isolated from apple and 85%–87% with Australian grapevine viroid (AGVd) isolated from grapevine. Taking into account the present concept of viroid species, we conclude that the viroid is AFCVd. Circumstantial evidence suggests that AFCVd from apples and hops were endemic in Japan only where cultivation of the two host plants overlapped, thereby strongly supporting the possibility that AFCVd (or an ancestral viroid) was transmitted across the species barrier from apples to hops or hops to apples somewhere in the region. Phylogenetic analysis of AFCVd from hops, AFCVd from apples, and AGVd together with the other members of the genus Apscaviroid revealed that the Akita isolates of AFCVd from hops (AFCVd-hop) formed a cluster that is distinct from AFCVd-apple and AGVd. Accumulation of host-specific sequence variation following their isolation in different host species may be leading to the formation of two viroid species from a common ancestor.     

Molecular and biological characterization of a severe isolate of <Emphasis Type="Italic">Tomato chlorotic dwarf viroid</Emphasis> containing a novel terminal right (T<Subscript>R</Subscript>) domain sequence

Tomato chlorotic dwarf viroid (TCDVd) manually inoculated to transgenic (cv.‘Desiree’) potato plants containing antimicrobial cationic peptides failed to develop symptoms in above ground plant parts, but infected tubers were symptomatic. Plants from the infected tubers (second generation plants) emerged as either severely stunted (bushy stunt isolate, BSI) or tall and symptomless. Molecular characterization of BSI isolates showed TCDVd sequence variants 95 to 98% identical to TCDVd sequences from the database, while a viroid variant identical to TCDVd type isolate (acc # AF162131) was cloned from symptomless plants. The TCDVd BSI variants had novel U165C, GU177-178AA, and UCAC181-184CUUU nucleotide substitutions in the terminal right (T_R) domain of the viroid molecule. The cloned viroid cDNAs of the BSI were infectious to experimental (cv. ‘Sheyenne’) tomato plants causing stunted plants with profuse auxiliary shoots. Visual evaluation of the susceptibility of the BSI to 18 potato and 21 tomato cultivars revealed severe symptoms in most cultivars of both species. The progeny variants accumulating in each potato and tomato cultivar exhibited the same novel T_R domain in most cultivars, with only a slight variation in a few. The severity of the stunting symptoms induced by TCDVd from BSI isolates in both potato and tomato cultivars has not been noted previously with other TCDVd isolates and, as such, it is proposed that this new isolate be recognized as a distinct genotype. Emergence of this type of sequence variant in commercial fields or commercial tomato greenhouses could potentially cause relevant losses in both crops.     

Characterization of a new Apple dimple fruit viroid variant that causes yellow dimple fruit formation in ‘Fuji’ apple trees

A 303-nucleotide viroid was isolated from an apple tree (Malus × domestica, ‘Fuji’) cultivated in Japan. The viroid had 84.9% overall nucleotide sequence homology to Apple dimple fruit viroid (ADFVd), a member of Pospiviroidae, reported from Italy. This viroid differed from the Italian variant by 47 mutations (38 substitutions, six deletions and three insertions), and most of these mutations occurred on either side of the central conserved region. The leaves and branches of the infected trees did not have any disease symptoms, but the fruits were dimpled and yellow. The infected scions were top-grafted onto a healthy ‘Fuji’ apple tree, which tested positive for this viroid in a northern hybridization analysis, and yellow dimple fruits were produced in the second growing season. We propose that this viroid is a new variant of ADFVd and causes yellow dimple fruit formation in ‘Fuji’ apple trees.     

Molecular characterization and phylogenetic analysis of <Emphasis Type="Italic">Citrus viroid VI</Emphasis> variants from citrus in China

Citrus viroid VI (CVd-VI) is a viroid originally found from citrus and persimmon in Japan. We report here the identification and molecular characterization of CVd-VI from four growth regions of China. A total of 90 cDNA clones from nine citrus cultivars were sequenced. The sequence homologies of the Chinese CVd-VI and the reference sequence (NC_004359) vary from 94.2% to 97%. The sequence homologies among the Chinese isolates were up to 95.2%. Phylogenetic analysis of the 23 CVd-VI variants from China and Japan showed that they were grouped into two clades, one with 20 citrus variants and another with three persimmon variants, regardless of the geographic origins. Therefore, as with Hop stunt viroid, CVd-VI could also be divided into two types, citrus and persimmon types. Sequence alignment showed that most nucleotide changes between the two clades occurred in the P, V and T_L domains, and analysis indicated that these mutations influenced the predicted secondary structures under minimum energy.     

Distribution and population diversity of <Emphasis Type="Italic">Australian grapevine viroid</Emphasis> (AGVd) in Turkish autochthonous grapevine varieties

Several viroid species have been reported to infect grapevine in Turkey and there has been not much about their genetic diversity, except Australian grapevine viroid (AGVd, genus Apscaviroid, family Pospiviridae). The viroid was recently detected in Turkish vineyards with very little information about its variability. Therefore, the autochthonous grapevine varieties in two major grape-growing areas in Turkey, i.e. the Eastern Mediterranean and the Southeast Anatolia regions were tested for the prevalance and genetic diversity. The presence of AGVd in the autochthonous varieties was verified by RT-PCR. The incidence of AGVd infection was relatively low in both regions due to self-rooted nature of the plants in the areas. Comparative analysis of local AGVd isolates from these native varieties was performed with viroidal genome sequences from NCBI database. Consequently, AGVd populations in Turkey contained five major sequence variants consisting of three varieties. Four variants had minor sequence variations while one was remarkably diverse.     

苹果锈果类病毒山东栖霞分离物的分子鉴定及序列分析

本研究以采自山东省栖霞市的两个苹果样品为试验材料,利用二维电泳、斑点杂交、RT PCR等分子生物学技术对样品中的苹果锈果类病毒(ASSVd)带毒情况进行了检测。结果表明：两个样品均携带ASSVd。对两个样品中的ASSVd进行克隆测序,并利用生物学软件DNAMAN对所得序列进行分析,结果表明：与世界上首次报道的ASSVd序列(X17696)相比,本研究所得到的ASSVd序列变异较小,相对比较保守。