Genetic diversity and a long evolutionary history of plum pox virus strain rec in Turkey

European Journal of Plant Pathology - Plum pox virus strain Recombinant (PPV-Rec) is hypothetically considered as homologous recombinant between strains PPV-M and PPV-D. The nucleotide position...     

Genetic diversity and molecular epidemiology of the T strain of Plum pox virus

Very limited information is available on the origin, diversity and evolution of Plum pox virus (PPV) ‘Turkey’ (T) strain. Phylogenetic analyses based on partial sequences of 421 isolates and complete genome sequences of 57 isolates, representing the geographical distribution of PPV-T in Turkey, revealed the existence of several monophyletic and, in some cases, geographically limited groups within the PPV-T strain (Ankara-Konya1-Kayseri, Ankara-Balkan, Istanbul, Konya2 and Balkan). PPV-T diversity (0.018%) was found to be greater than that of PPV strains D and Rec but lower than that of the M strain when including the newly described and divergent M-Istanbul isolates, suggesting a long evolutionary history for PPV-T. The European part of Turkey in the Balkans, close to Bulgaria where PPV was identified for the first time, appears as a likely centre of origin for PPV-T isolates. The colonization of various parts of Turkey by diverse isolates from that region, followed by secondary local spread, is the most likely scenario for the diffusion of PPV-T in Turkey.     

Plum pox virus detection in dormant plum trees by PCR and ELISA

An immunocapture polymerase chain reaction (IC-PCR) protocol and ELISA were compared for their effectiveness in detecting plum pox virus (PPV) in dormant plum material. Although the IC-PCR was about one thousand times more sensitive than ELISA, PPV was detected by ELISA in 71–80% of bark samples collected in December, January and March 1996/97 from pot-grown rootstock trees inoculated with PPV the previous March, compared with 85–86% detection in the same samples by IC-PCR. In similar samples from one-year-old shoots taken from infected branches of orchard trees, 66–81% were positive by ELISA compared with 81–87% by IC-PCR. With bulked samples taken from the fibrous roots of the pot-grown trees, PPV was detected in 92–100% of samples by IC-PCR in winter compared with only 38–65% by ELISA. These results were confirmed in samples from the roots and shoots of the same trees in 1997/98. Three samples per shoot would have been sufficient to detect PPV by ELISA in 87 of the 88 infected shoots tested during the two winters. However, infected shoots are irregularly distributed in diseased trees and PCR assays of root samples offer the potential for improving the reliability of identifying trees infected with PPV.     

Diversity of Plum pox virus isolates in Bosnia and Herzegovina

Sixteen Plum pox virus (PPV) isolates from several stone fruit cultivars, host species, orchards and geographical areas of Bosnia and Herzegovina were selected for typing, using serotype-specific monoclonal antibodies (MAbs) and PCR–RFLP, targeting the 3' terminal region of the coat protein (CP) and P3-6K₁ with restriction enzymes Rsa I and Dde I. Four PPV isolates were identified as PPV-M by serology and PCR; eight isolates were identified as PPV-D based on PCR–RFLP on both genomic regions, but were not recognized by the D-specific MAb4DG5. Four isolates from plum were identified as natural D/M recombinants (PPV-Rec), based on conflicting results of CP and P3-6K₁ typing. To investigate the genetic diversity of Bosnian PPV isolates in more detail, five isolates (three PPV-Rec, one PPV-M and one PPV-D) were partially sequenced in the region spanning the 3' terminal part of the NIb gene and the 5'-terminal part of the CP gene, corresponding to nucleotides 8056–8884. Nucleotide sequence alignment of recombinant isolates showed that they were closely related at the molecular level to previously characterized recombinants from other European countries, and shared the same recombination break point in the 3' terminal part of the NIb gene. This is the first report of naturally infected Prunus trees with PPV-M, PPV-D and PPV-Rec in Bosnia and Herzegovina. The high variability of the Bosnian PPV isolates fits with the presence of this virus in the country over a long period.     

Production and characterization of a monoclonal antibody specific to the M serotype of plum pox potyvirus

A monoclonal antibody to an Albanian isolate of plum pox potyvirus (PPV) was obtained (MAbAL), that specifically recognized strain M of this virus. The specificity of MAbAL, assessed by comparative ELISA on 130 PPV isolates of different geographical origin, 22 of which were also tested by comparative IC-PCR, gave consistent and highly reproducible results. MAbAL seems to be elicited by a stable surface determinant that makes it particularly suitable for successful use under a wide range of conditions. MAbAL is an useful addition to the panel of PPV-specific MAbs available to date.     

Systemic spread of Plum pox virus (PPV) in Mariana plum GF 8-1 in relation to shoot growth

Infection of Prunus spp. by Plum pox virus (PPV) is characterized by an uneven distribution of the virus within the tree and branches. In order to gain a better understanding of this distribution, a method for modelling tree growth was used. PPV spread was followed within susceptible Mariana plum clone GF 8-1 shoots for 4 months after inoculation. Shoot growth was unaffected by the presence of the virus. Symptoms appeared on leaves produced in the most actively growing parts of the shoots, i.e. at the beginning of the season. PPV was detected in leaves other than those showing symptoms. The proportion of leaves with detectable virus decreased from the zone showing symptoms, with 100% ELISA-positive responses, to the shoot tip with no detectable virus in leaves produced between 111 and 127 days after inoculation. Furthermore, a higher proportion of positive ELISA results was obtained below the zone showing symptoms (77%) compared with 50% above. PPV was detected in 95% of the most vigorous shoots 71 days after inoculation compared with 37% of slower-growing, later-produced shoots.     

First detection and complete genome characterization of a Cherry (C) strain isolate of plum pox virus from sour cherry (Prunus cerasus) in Germany

Journal of Plant Diseases and Protection - An isolate of plum pox virus (PPV) was detected in sour cherry (Prunus cerasus) in the Eastern region of Germany. Symptoms observed on infected sour...     

Genetic variation and evolutionary analysis of Pepino mosaic virus in Sicily: insights into the dispersion and epidemiology

Pepino mosaic virus (PepMV) is a highly infectious potexvirus that causes a severe disease in tomato (Solanum lycopersicum) crops worldwide. In Sicily, the first outbreak was detected in a single greenhouse in 2005 and it was promptly eradicated. However, in 2008, a large number of greenhouses were simultaneously affected, and it was impossible to eradicate or control the virus. This study addressed the dispersion and the genetic diversity of PepMV isolates obtained from the outbreak in Sicily, in comparison with worldwide PepMV isolates, to gain insight into the factors determining the evolution and epidemiology of the virus. A total of 1800 samples from plants with and without symptoms were collected in the Sicilian provinces of Agrigento, Caltanissetta, Palermo, Ragusa, Siracusa and Trapani. Three isolates collected at different times were biologically characterized. The incidence of the virus increased rapidly from 13% in 2011 to 63% in 2013, and phylogenetic analysis showed that all Sicilian isolates of PepMV belonged to the CH2 strain, one of the six strains previously described. Nucleotide diversity of the Sicilian isolates was low, thus suggesting rapid spread and genetic stability.     

山西苹果茎痘病毒遗传多样性分析

苹果茎痘病毒是苹果安全生产的巨大威胁,严重影响苹果产量和质量。探讨苹果茎痘病毒(Apple stem pitting virus, ASPV)在山西省的分布、变异和多样性,可为制定可持续的病毒管理策略提供理论依据。从山西省11个地区采集苹果叶片样品进行RT-PCR检测。结合在线数据库,利用相关软件对文中研究获得的序列进行系统发育、遗传多样性、重组以及种群遗传分化等分析。RT-PCR检测结果显示从山西省11个地区采集的409份苹果叶片样品中,ASPV的检出率为36.33%(临漪)至55.37%(平遥)。选择15个ASPV检测为阳性的样品,分别克隆其CP基因并与22个不同的ASPV分离物进行核苷酸和氨基酸一致性分析,发现37个ASPV分离物的核酸一致率为70.27～96.31%,氨基酸一致率为37.04～96.64%,其中,Shanxi-2与JX673826.1的核酸一致率最高,为90.86%, Shanxi-2与MN617853.1的核酸一致率最低,为70.40%。基于CP的进化树分析结果显示37个ASPV分离物被划分为2个进化群体。遗传多样性分析结果表明ASPV种群发生了收缩,且在两个...     

马铃薯Y病毒在种薯中检出率及其株系鉴定

 马铃薯是我国重要粮食和经济作物。马铃薯Y病毒(potato virus Y,PVY)是危害马铃薯生产的重要病害。种植脱毒种薯是防治PVY最有效的途径。马铃薯种薯携带PVY问题严重,但种薯中PVY株系还不清楚。本研究利用PVY特异性抗体检测了7个马铃薯品种362个种薯,发现不同品种种薯带毒率差异较大,最高达12%。通过RT-PCR方法扩增获得了7个PVY分离物编码区全序列。重组分析发现7个分离物基因组均为重组型,根据重组位点的差异可以分为PVY^NTN-NW(SYR-II型)、Rec-1、Rec-2和Rec-3等4种重组类型,后3种为新重组类型。系统进化分析发现,分离物HQH18G3-10与PVY^NTN-NW(SYR-II型)处于同一个大的分支,但与中国PVY大田分离物聚集在一起形成一个相对独立的组,命名为PVY^NTN-NW(CN型);其余6个分离物与数据库中的中国分离物聚集在PVY^N-Wi组。这暗示PVY中国分离物具有相对独立的进化过程,PVY马铃薯大田分离物和种薯分离物进化上相近。所有分离物均能在珊西烟上引起典型叶脉坏死症状,HQH18G3-10引起的坏死症状最为严重。本研究首次报道了我国种薯内PVY发生情况,对分析病毒发生发展规律和防控具有借鉴作用。     

马铃薯Y病毒在种薯中检出率及其株系鉴定

马铃薯是我国重要粮食和经济作物。马铃薯Y病毒(potato virus Y,PVY)是危害马铃薯生产的重要病害。种植脱毒种薯是防治PVY最有效的途径。马铃薯种薯携带PVY问题严重,但种薯中PVY株系还不清楚。本研究利用PVY特异性抗体检测了7个马铃薯品种362个种薯,发现不同品种种薯带毒率差异较大,最高达12%。通过RT-PCR方法扩增获得了7个PVY分离物编码区全序列。重组分析发现7个分离物基因组均为重组型,根据重组位点的差异可以分为PVY^NTN-NW(SYR-II型)、Rec-1、Rec-2和Rec-3等4种重组类型,后3种为新重组类型。系统进化分析发现,分离物HQH18G3-10与PVY^NTN-NW(SYR-II型)处于同一个大的分支,但与中国PVY大田分离物聚集在一起形成一个相对独立的组,命名为PVY^NTN-NW(CN型);其余6个分离物与数据库中的中国分离物聚集在PVY^N-Wi组。这暗示PVY中国分离物具有相对独立的进化过程,PVY马铃薯大田分离物和种薯分离物进化上相近。所有分离物均能在珊...     

Detection and characterization of phytoplasmas in diseased stone fruits and pear by PCR-RFLP analysis in Turkey

During the late summer-early autumn of 2002, surveys were carried out in Turkey to determine the presence of phytoplasma diseases in fruit trees. Phytoplasmas were detected and characterized by PCR-RFLP analysis and TEM technique in stone fruit and pear trees in the eastern Mediterranean region of the country. Six out of 24 samples, including almond, apricot, peach, pear and plum, gave positive results in PCR assays. RFLP analysis usingSspI andBsaAI enzymes of PCR products obtained with primer pair f01/r01 enabled identification of the phytoplasmas involved in the diseases. Stone fruit trees, including a local apricot variety (‘Sakıt’) and a pear sample, were found to be infected with European stone fruit yellows (ESFY, 16SrX-B) and pear decline (PD, 16SrX-C) phytoplasmas, respectively. This is the first report in Turkey of PD phytoplasma infecting pear and of ESFY phytoplasma infecting almond, apricot, myrobalan plum and peach; ESFY phytoplasma infecting Japanese plum was previously reported. http://www.phytoparasitica.org posting July 21, 2005.     

鳞翅目昆虫迁飞相关基因的鉴定及进化分析

为明确迁飞性昆虫迁飞行为的分子调控机制,选取12种鳞翅目昆虫为研究对象,将其分为迁飞组和非迁飞昆虫组,采用PAML软件分析单拷贝直系同源基因在2个分组中的进化速率,从基因组水平对涉及生物钟调节、神经调节和内分泌调节3类迁飞相关基因进行注释和比较。结果表明,部分基因在迁飞昆虫和非迁飞昆虫中的进化速率存在显著差异,且这些基因富集在肌肉结构发育、复眼及光感细胞发育、能量代谢、腺体发育、醇酮类及脂蛋白合成代谢、磷酸化调节等生物过程中;与神经调节相关的基因在迁飞昆虫中有不同程度的显著扩增或收缩,而涉及生物钟调节的基因中仅ebony在迁飞组昆虫中的拷贝数显著多于非迁飞组的拷贝数,与内分泌调节相关的法尼醇脱氢酶编码基因在迁飞组和非迁飞组中呈现显著差异。表明迁飞和非迁飞2组昆虫在基因组水平上存在部分基因拷贝数增加或减少的规律,可能是迁飞昆虫或非迁飞昆虫的共同特征。     

番茄黄化曲叶病毒的鉴定与群体进化分析

番茄黄化曲叶病(tomato yellow leaf curl disease,TYLCD)是番茄上的重要病害,可由多种双生病毒引起。为了明确北京地区番茄黄化曲叶病的病毒种类和病毒基因组变异情况,本研究收集了51个采自北京不同区县的病毒疑似样品,进行了双生病毒的检测及分离物的基因组分析。经双生病毒简并引物检测25个样品呈阳性;扩增获得10个代表性分离物的全基因组,大小均为2 781bp,共含有6个开放阅读框;经比对,10个分离物与Tomato yellow leaf curl virus-Israel(TYLCV-IL)同源率大于99%;基于我国TYLCV分离物全基因组序列的变异分析表明,TYLCV在进化上比较保守,整个基因组上的变异是不均匀的;系统发育树显示我国TYLCV分离物在进化树上可分为3个组群,分析了我国TYLCV群体进化情况。     

巴氏新小绥螨溴氰菊酯抗药性品系对常见药剂的交互抗性及其种群参数分析

为了明确巴氏新小绥螨Neoseiulus barkeri溴氰菊酯抗性品系对常用杀虫(螨)剂的交互抗性水平及生物适合度,为巴氏新小绥螨抗药性品系田间应用提供科学依据。本文应用玻片浸渍法测定了巴氏新小绥螨溴氰菊酯抗性品系对12种杀虫(螨)剂的交互抗性,采用种群生命表评价了其生长发育及繁殖情况。结果显示,相对于巴氏新小绥螨敏感品系,溴氰菊酯抗性品系(226.38倍)对供试的其他6种拟除虫菊酯类药剂均存在交互抗性,尤其对氯氟氰菊酯的交互抗性倍数最高,达到2 210.91倍。对噻虫嗪、毒死蜱和乙螨唑的交互抗性分别是116.46、110.71倍和20.43倍,对丁硫克百威、阿维菌素和哒螨灵无交互抗性。对其生物适合度研究发现,溴氰菊酯抗性品系相较于敏感品系,前若螨期和产卵前期显著缩短,产卵期和单雌总产卵量显著增加。上述结果表明,巴氏新小绥螨溴氰菊酯抗性品系对10种常用杀虫(螨)药剂产生了不同水平的交互抗性,且其繁殖率显著增加,推荐在田间推广应用。     

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。     

Genetic variation and evolutionary forces shaping Cucumber vein yellowing virus populations: risk of emergence of virulent isolates in Europe

The genetic variation and evolutionary mechanisms shaping Cucumber vein yellowing virus (CVYV) populations were investigated by analysis of nucleotide sequences coding for P1b, P1b/P3 and coat proteins (CP) from isolates collected in different countries. The complete genome sequence of isolate ISM from Israel was also determined and compared to those of isolates Jor from Jordan and ALM32 from Spain. This isolate had overall nucleotide identities of 94·23 and 94·96% with ALM32 and Jor, respectively. Nucleotide variation among isolates was not homogeneously distributed, with the 5′ half of the genome being more variable than the 3′ half. A Bayesian phylogenetic tree of the CP showed that CVYV isolates clustered into two main clades: isolates from the Middle East region (Lebanon, Israel and Jordan) clustered in both clades whereas the isolate from Tunisia clustered in clade I and the European isolates clustered as a homogeneous phylogroup in Clade II. A similar topology was observed for P1b but with incongruences with respect to the CP, suggesting genetic exchange among virus isolates, which were confirmed with recombination algorithms. The low genetic diversity within the European phylogroup with respect to the other isolates, neutralist tests and genetic differentiation analyses suggest that the Middle East region is the cradle of CVYV and that a unique virus introduction event occurred in Europe, where the virus spread rapidly. Taken together, these findings indicate a risk of emergence of virulent CVYV isolates in Europe either through migration from the Middle East or by genetic changes of the European isolates.     

Towards an integrative biology research: a case study on adaptive and evolutionary trends of Miscanthus populations in Taiwan

A program of research named Towards an Integrative Biology (TAIB) has recently been promoted by the International Union of Biological Sciences, involving multidisciplinary and interdisciplinary research. Studies of Miscanthus plants which emphasized the TAIB theme were undertaken. Miscanthus species are the most widely distributed and dominant species in Taiwan, growing everywhere from the coastal to mountainous areas, and from agricultural to polluted land. Particularly, the grasses grow well in habitats under environmental stresses. Physiological and genetic adaptations are fundamental mechanisms for these grasses' survival in stressful environments. Findings based on field measurements and laboratory analyses were able to elucidate some of the mechanisms of grasses adapted to stressful environments. Adaptive radiation occurred when most niches were open during the postglacial periods. Particularly, population discontinuity of the grasses was found on the Orchid and Green islets of Taiwan. Likewise, Miscanthus sinensis var. glaber and var. formosanus occupied lands from low to middle elevations of Taiwan, while Miscanthus transmorrisonensis appeared in the highlands above 2400 m. Phylogenetically, Miscanthus has evolved into various ecotypes, varieties and species in Taiwan as well as in other parts of Asia. The grass then evolved into Miscanthus floridulus , M. sinensis var. formosanus , Miscanthus flavidus , then to M. transmorrisonensis . Furthermore, the phylogeny of the Miscanthus sinensis complex of Taiwan was reconstructed by cladistic analysis on nucleotide sequences of nuclear ribosomal DNA internal transcribed spacers (nrDNA ITS) region and atpB - rbc L non-coding spacer of the chloroplast DNA. Rooted at M . floridulus the monophyly of M . sineneis was significantly supported by molecular evidence. The origin of this complex could be dated to the last glacial withdrawal about 20 000 years ago.     

太子参蚕豆萎蔫病毒2号CP基因的遗传多样性及分子进化分析

为了解太子参蚕豆萎蔫病毒2(Broad bean wilt virus 2,BBWV2)的遗传多样性及分子进化关系,本研究对5个不同地理来源的6份太子参病叶样品进行了BBWV2外壳蛋白(coat protein,CP)基因的RT-PCR扩增和克隆。序列分析结果表明,所得13条太子参BBWV2 CP基因序列均为1 345 bp,其核苷酸序列同一性在81.0%~99.0%之间,氨基酸序列同一性在93.5%~99.3%之间;核苷酸多样性为0.084 00;存在280个核苷酸多态性位点,其中232个为地域特异性位点;总变异数为278个,其中同义突变29个,异义突变249个。不同地理来源的太子参BBWV2分离物之间遗传分化程度较高,基因交流不频繁,遗传漂变可能导致分离物间明显的遗传分化。在系统进化树中,太子参分离物的聚类呈现出明显的地域特异性,江苏、贵州、湖南、福建分离物均聚类在I-a亚组,而山东分离物聚类在II-c亚组,遗传距离较远。研究表明,太子参BBW V2存在很高的遗传变异,基因突变是其产生遗传多样性的主要驱动力,而地理因素与其具有较高的核苷酸多样性密切相关。     

陕西省番茄黄化曲叶病毒基因间隔区缺失突变体的鉴定与不同分离物间群体进化研究

为明确番茄黄化曲叶病毒(tomato yellow leaf curl virus, TYLCV)基因组的变异情况, 分别从陕西省杨凌区?泾阳县?大荔县和阎良区采集了表现为番茄黄化曲叶病症状的抗病品种番茄样品20份以及感病品种番茄样品4份?经TYLCV特异性引物检测, 24个样品均为阳性?通过全长扩增测序获得了15个TYLCV分离物的基因组序列?序列分析显示, 其中7个分离物基因组大小为正常的2 781 bp, 而有8个TYLCV分离物基因组大小为2 768 bp?与正常基因组相比, 这8个分离物在基因间隔区(intergenic region, IR)的TATA-box与保守9核苷酸序列之间发生了13个核苷酸的缺失?对我国不同地区TYLCV分离物全基因组序列进行变异分析, 发现IR区域是发生核苷酸变异最大的区域?系统进化分析表明, 本研究分离到的15个TYLCV分离物均属于TYLCV-Israel进化分支下的中国亚群, 其中8个TYLCV IR缺失突变体与国内已报道的IR缺失突变体BJ04和BJ06亲缘关系较远, 而与本研究中分离得到的正常TYLCV分离物亲缘关系最近, 疑似为陕西地区出现的一类新TYLCV IR缺失突变体?本研究首次对我国不同地区多个TYLCV分离物出现IR区缺失现象进行了报道?