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Euphresco project VirusCollect – fulfilling the need for a common collection of plant viruses and viroids for reference 
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下载免费PDF全文 J. W. Roenhorst C. Lacomme C. Nisbet T. Leichtfried W. Menzel S. Winter R. A. A. van der Vlugt 《EPPO Bulletin》2017,47(1):41-47
The availability and accessibility of suitably characterized plant virus and viroid isolates for reference is vital for research and diagnostic laboratories. To ensure the long‐term availability of isolates and reference materials, there is a need for international collaboration. The Euphresco (European Plant Health Research Coordination) project VirusCollect aimed to establish a platform to link collections of viruses and viroids maintained by individual institutions via Q‐bank ( http://www.q-bank.eu/ ), a database on plant pests and diseases. Within the VirusCollect project, standard operating procedures were developed and implemented by the participating laboratories to guarantee the quality of isolates and data. In addition, over 135 virus and viroid isolates of phytosanitary and/or economic importance were added to Q‐bank, which now provides links to over 500 virus isolates of almost 100 species, in addition to basic information on many more plant viruses. VirusCollect has enabled the first step in collaboration between curators and standardization of maintenance of virus collections. The project established the basis for improving the quality of individual collections and the layout of Q‐bank as a platform to share data and information. The follow‐up project, VirusCollect II, enables further international collaboration to ensure future access to reliable collections of plant viruses and viroids. 相似文献
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DNA barcoding protocols for selected EU‐regulated arthropods, bacteria, fungi, nematodes and phytoplasmas were developed within the Quarantine organisms Barcoding of Life (QBOL) project financed by 7th framework program of the European Union. DNA barcodes generated with the developed protocols were stored in the Q‐bank database. An test performance study (TPS) was set up involving 14 participating laboratories to validate the use of the developed protocols as a diagnostic tool and to identify possible difficulties in the use of the protocols and Q‐bank. This paper describes the steps that were used to set up the TPS, to validate the protocols and to identify difficulties. TPS data shows that the developed tests are very robust and produce highly reproducible results. Participants managed to define good consensus sequences which allowed them to correctly identify their samples using Q‐bank in 78% of all cases. Q‐bank outperformed NCBI and BOLD in terms of diagnostic sensitivity and diagnostic specificity for all organism groups. Using general qualifiers, performance criteria and feedback from TPS participants, difficulties in the set‐up of the TPS, the use of the protocols and databases, and the proficiency of participants were identified/evaluated and recommendations for future work were made. The developed DNA barcoding protocols and Q‐bank have proven to be useful tools in support of the identification of selected EU‐regulated plant pests and pathogens on the desired taxonomical level. 相似文献
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目前, 我国梅树上的病毒种类及发生情况仍不完全清楚。本研究从北京、武汉、南京和无锡的梅园中采集了64份疑似感染病毒的叶片样品, 通过RT-PCR和斑点杂交, 对7种病毒和2种类病毒进行了检测。共检测到6种病毒和1种类病毒。其中, 李属坏死环斑病毒(prunus necrotic ringspot virus, PNRSV)和桃潜隐花叶类病毒(peach latent mosaic viroid, PLMVd)为我国梅树上的首次检出。PNRSV、亚洲李属病毒2号(Asian prunus virus 2, APV2)、桃叶痘伴随病毒(peach leaf pitting-associated virus, PLPaV)的检出率高于30%。综合考虑病毒的分布及检出率, PLPaV、APV2、PNRSV和李树皮坏死茎痘伴随病毒(plum bark necrosis stem pitting-associated virus, PBNSPaV)是武汉、南京和无锡梅树上的主要病毒。此外, 通过克隆和测序, 获得了PLMVd和梅树病毒A(mume virus A, MuVA)的基因组, PLPaV的RNA1组分和PNRSV外壳蛋白(CP)基因序列。序列比较分析显示, 我国PLMVd梅分离物和PNRSV梅分离物与我国桃分离物亲缘关系最近, 表明PLMVd和PNRSV可能在梅和桃树间交互侵染;我国MuVA梅分离物序列与日本梅分离物序列的相似性高达98.56%;PLPaV梅分离物与我国桃分离物之间序列变异较大。上述结果不仅进一步明确了我国梅树上的病毒及类病毒种类和分布情况, 而且有助于深入了解它们的流行与传播。 相似文献
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Many laboratories maintain historical collections of preserved plant virus isolates that store a wealth of untapped data, including original type isolates, studied in the pre-sequencing era. Currently, many recently recognized virus species exist with no supporting reference sequences. Also, many virus sequences appear new when compared to available sequences, but, on sequencing pre-sequencing era isolates, they may coincide. Such linkages allow access to data from previously determined biological and other parameters from pre-sequencing era studies. These linkages are increasingly being found using high-throughput sequencing, helping clarify virus taxonomy and improving understanding of virus ecology and evolution. Thus, mistakes can be avoided in naming viruses and in combining or separating them, as well as enabling identification of unknown viruses preserved long ago. With well-established viruses, success in dating and other evolutionary studies, and discovery of changes in regional virus populations, both depend upon comparisons between recent and old isolate sequences covering the greatest possible time periods. Such studies help reveal the extent that human activities have influenced virus evolution and changed virus populations on a global scale. Sequencing virus genomes from herbarium specimens, archaeological specimens, or living plant collections can provide complementary data. By bringing context to newly detected viruses and supporting plant pest risk analyses, linking new virus discoveries to previously generated disease symptom, host range, virus transmission, and geographical distribution data has important implications for plant health regulation. Also, historical isolates can provide an invaluable resource facilitating biosecurity investigations involving virus introductions, entry pathways, and baseline surveillance. 相似文献
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A novel pair of universal primers was developed to detect potyvirus species after conserved sites were identified using all full‐length potyvirus sequences available by 2005. The breadth of specificity of the new primers, NIb2F and NIb3R, was investigated and compared with the specificity of two routinely used primer pairs in plant virus diagnostic laboratories. RNA from 40 potyvirus isolates representing 23 recognized and three possible new species was tested. Reactions with NIb2F and NIb3R produced amplicons of 350 bp from all 40 virus isolates tested. Reactions with the previously published WCIEN and Potyvirid primers amplified cDNA from 32 and 21 isolates, representing possibly 21 and 15 species, respectively. The identity of 12 unknown potyvirus isolates was confirmed by sequencing and three were found to be potentially distinct potyvirus species. Gel banding patterns from reactions with NIb2F and NIb3R were simpler to interpret than those from reactions with the other two primer sets; fewer products were visible and the cDNA fragments were less variable in size. RT‐PCR with the novel primers is predicted to be able to detect virus isolates from all major groups within the genus Potyvirus and its reliability makes it well suited for use as a routine diagnostic assay. 相似文献
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Test plants are often used for broad screening for plant viruses. Mechanical inoculation of a series of test plants enables generic detection of mechanically transmitted viruses in only 1 assay. Moreover, such an assay is suitable for known as well as unknown viruses and their variants. However, in comparison to serological and molecular methods, quality control in bioassays is almost never addressed. The system of positive and negative controls, blind samples and proficiency tests is applicable, provided that a broader interpretation of positive and negative controls is used. For validation, performance criteria can only be determined for individual viruses. However, results can often be extrapolated. Sensitivity is addressed by dilution and expressed as a relative value. Specificity has to consider the virus species and the plant species to be tested. Selectivity mostly depends on the plant species tested, because some hosts contain components that inhibit transmission. Repeatability and reproducibility, determined for a limited number of samples, appears high, as also substantiated by the authors' experience. This paper details how EPPO Standards on quality control were implemented by the National Plant Protection Organization of the Netherlands (NPPO‐NL). This information will be of use for other laboratories that wish to introduce quality control in bioassays for virus testing. 相似文献
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我国49种线状植物病毒分子鉴定及其基因组研究 总被引：1，自引：0，他引：1
本研究建立了马铃薯Y病毒属、马铃薯X病毒属、麝香石竹潜隐病毒属和葱X病毒属成员RT-PCR检测和全基因组扩增技术体系,并成功用于60多种供试植物病毒的检测诊断。利用所建立的技术体系,从全国18个省市42种作物上采集的病样中鉴定了49种植物病毒,其中10种为新种,11种为国内新记录,更正了7种病毒的鉴定和命名。测定了这49种病毒217个分离物基因组序列,并全部在国际基因数据库登录,占全球登录的植物病毒基因组序列总数的3.8%,其中27种植物病毒为基因组全序列,20种为国际首次报道,15种病毒全序列被美国国家生物技术信息中心(NCBI)确定为相关病毒的标准序列。 相似文献
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Kang S Ayers JE Dewolf ED Geiser DM Kuldau G Moorman GW Mullins E Uddin W Correll JC Deckert G Lee YH Lee YW Martin FN Subbarao K 《Phytopathology》2002,92(3):232-236
ABSTRACT A better understanding of the phenotypic and genetic diversity of significant agricultural pathogens and how their populations change in the field is critical for designing successful, long-term disease management strategies. Although efforts to determine the genetic diversity of plant pathogens have substantially increased in recent years, mainly due to the availability of various molecular tools, complementary efforts to archive and integrate the resulting data have been very limited. As a consequence, it is often difficult to compare the available data from various laboratories because the data have been generated by diverse tools, often preventing any direct comparisons, and are saved in a format that is unsuitable for comparative studies. The establishment of an internet-based database that cross-links the digitized genotypic and phenotypic information of individual pathogens at both the species and population levels may allow us to effectively address these problems by coordinating the generation of data and its subsequent archiving. We discuss the needs, benefits, and potential structure of such a database. 相似文献
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M. M. Finetti Sialer G. Parrella M. Papanice C. Vovlas D. Gallitelli 《EPPO Bulletin》2000,30(2):301-304
An account is given of strain‐specific diagnostic methods currently adopted in Italy to detect alfalfa mosaic alfamovirus (AMV), cucumber mosaic cucumovirus (CMV) and tomato spotted wilt tospovirus (TSWV). These viruses are highly detrimental to tomato crops as the introduction of new virus strains has deeply changed the population structure of resident viruses. RT‐PCR coupled with restriction analysis of amplicons proved suitable for differentiating CMV and AMV strains whereas single‐stranded conformational polymorphism (SSCP) was used for the identification of TSWV isolates. Application of strain‐specific diagnostic methods to phytosanitary inspection of plant propagules is suggested as a powerful tool for timely identification of new virus strains 相似文献
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G. Loconsole M. Saponari F. Faggioli G. Albanese H. Bouyahia T. Elbeaino A. Materazzi M. Nuzzaci V. Prota G. Romanazzi N. Trisciuzzi V. Savino 《EPPO Bulletin》2010,40(3):423-428
Sanitary selection and certification of olive cultivars require sensitive diagnostic methods and effective sanitation protocols. Although much attention has been paid in the past few years to the development of diagnostic tools for reliable virus identification, the need to define a common and standardized diagnostic protocol led to the implementation of a ring test among nine Italian diagnostic laboratories. A one‐step RT‐PCR protocol and different primer sets, targeting the most common olive viruses covered by phytosanitary rules, were tested in each laboratory, using the same batch of positive and healthy controls as well as the same amplification conditions and reaction components. The one‐step RT‐PCR, performed using several specific primer sets, was able efficiently to detect the target viruses in all laboratories. Furthermore, a one‐step RT‐PCR protocol was used successfully for the first time for detection of Tobacco necrosis virus (TNV) and Olive mild mosaic virus (OMMV). Results showed that all target viruses were not uniformly distributed in the canopy, and that at least two subsets of samples must be collected from each plant. This standardized protocol is now being used to produce nuclear stocks for 70 different Italian olive cultivars, in the framework of the national project OLVIVA, which involves 25 national research institutions. 相似文献
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This paper describes the database Q‐bank ( www.q-bank.eu ). This freely accessible database contains data on plant pathogenic quarantine organisms to allow fast and reliable identification. Development of accurate identification tools for plant pests is vital to support European Plant Health Policies. Council Directive 2000 ? 29 ?EC lists approximately 300 entries representing a large number of species (e.g. non‐European Tephritids contains approximately 3500 species) for which protective measures, against introduction and their spread within the European Community, need to be taken. The risk of introduction of pests into the European Union is increasing because of the increase in the volumes, commodity types and origins of trade, the introduction of new crops, the continued expansion of the EU, the numbers of international travellers and the impact of climate change. Identifying pests (in particular new emerging pests) requires staff with specialised skills in all disciplines (mycology, bacteriology etc.), which is only possible within large centralised laboratory facilities. Expertise in taxonomy, phytopathology and other fields in plant health, which are vital for sustaining sound public policy on phytosanitary issues, are under threat. Sharing knowledge on regulated and non‐regulated pests is necessary to manage a cost‐effective and efficient plant health system in the context of expanding globalisation of trade in plant material. 相似文献
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For several years work has been ongoing to compile information to facilitate the identification of non‐native plants that (potentially) pose a threat to the biodiversity of the ecozone comprising Northern Germany, the Netherlands, Belgium and North‐Western France. Such identification information may also be used for species that are regulated by other countries and are likely to be present as contaminants in commercial exports originating from the Netherlands. This information system comprises a set of interactive image‐driven identification keys for invasive plants at various growth stages for use in a range of different situations: seed contaminants in bird feed, weeds in bonsai plants, seedling identification, identification keys of invasive terrestrial plants and invasive aquatic plants. The advantage of image‐driven identification keys using a multiple entry system lies in limiting misunderstandings in terminology and failure in identification, in the absence of certain characters, as is sometimes the case in dichotomous keys. The interactive keys are linked to the species information in the Q‐bank database, including datasheets, worldwide distribution maps, specimen level information, barcodes of selected species, etc. This information is now available at http://www.q-bank.eu/Plants/ 相似文献
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Production of anti-virus,viroid plants by genetic manipulations 总被引：1，自引：0，他引：1
Ishida I Tukahara M Yoshioka M Ogawa T Kakitani M Toguri T 《Pest management science》2002,58(11):1132-1136
Many pathogenic plant viruses are RNA viruses, which initiate production of double-stranded RNA intermediates when they replicate in host plant cells. Introduction of double-stranded RNA-specific ribonucleases such as the Schizosaccharomyces pombe derived pac I protein and animal cell derived interferon-induced 2',5'-oligoadenylate synthetase (2-5 Aase)/ribonuclease L (RNase L) system into various plants may make plants resistant to various pathogenic viruses and viroids. We have demonstrated that pac I and 2-5 Aase/RNase L transgenic tobacco plants are resistant to various viruses including tobacco mosaic virus, cucumber mosaic virus and potato virus Y. In addition, pac I transgenic potato plants are resistant to potato spindle tuber viroid. Using Agrobacterium-mediated transformation, we have established a transformation system for chrysanthemum plants and have recently developed pac I transgenic chrysanthemum (Dendranthema grandiflora cv Reagan) resistant to chrysanthemum stunt viroid and have grown them in isolated fields for an evaluation of their effects. 相似文献
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In 2004, the EPPO Council expressed profound concerns about the decreasing expertise in plant protection and declared a state of emergency for Plant Health (‘Madeira declaration’). As diagnostics is one of the scientific fields which are vital for sustaining sound plant health policies, a questionnaire was launched and all EPPO member countries were asked to provide information about their diagnostic expertise, focusing on regulated pests or pests which may present a risk to the EPPO region. In 2006, results of the questionnaire were analysed and compiled by the EPPO Secretariat into a new database. This database now contains detailed information (contact addresses, quality programmes, and accreditations) for 80 diagnostic laboratories from 28 EPPO member countries. More than 500 experts are now registered with details about their diagnostic expertise (pests diagnosed and methods used). The EPPO database on diagnostic expertise can be freely accessed on the Internet: http://dc.eppo.org . 相似文献
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Giorgio Gambino Beatriz Navarro Rosalina Vallania Ivana Gribaudo Francesco Di Serio 《European journal of plant pathology / European Foundation for Plant Pathology》2011,130(4):511-519
Indirect somatic embryogenesis is effective at eliminating the most important viruses affecting grapevines. Accordingly, this
technique was tested as a method for eradicating two widespread viroids, Grapevine yellow speckle viroid 1 (GYSVd-1) and Hop stunt viroid (HSVd), from four grapevine cultivars. Both viroids were detected by RT-PCR in grapevine floral explants used for initiating
embryogenic cultures, as well as in undifferentiated cells of embryogenic and non-embryogenic calli from anthers and ovaries.
In contrast, somatic embryos differentiated from these infected calli were viroid-free, and viroids were not detected in embryo-derived
plantlets even 3 years after their transfer to greenhouse conditions. A wider spatial distribution of HSVd than GYSVd-1 within
proliferating calli was revealed by in situ hybridization, whereas no hybridization signal was detected in the somatic embryos.
In addition, GYSVd-1 and HSVd were localised in the nucleus of infected cells, conclusively showing the nuclear accumulation
of representative members of Apscaviroid and Hostuviroid genera, which has been only an assumption so far. Somatic embryogenesis was compared to in vitro thermotherapy, a technique
routinely used for virus eradication. After thermotherapy, HSVd and GYSVd-1 were detected in all in vitro plantlets of the
cultivar Roussan, and in all lines analysed after 3 years of culture in greenhouse. The high efficiency with which somatic
embryogenesis may eliminate viroids and viruses from several infected grapevine cultivars, should allow the availability of
virus- and viroid-free material, which would be useful not only for sanitary selection but also for basic research on plant-virus
and plant-viroid interactions in grapevine. 相似文献
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Shall we share? A repository for Open Research Data in agriculture and environmental sciences 下载免费PDF全文
下载免费PDF全文 Many initiatives actively encourage investigators to make their research data available, but the process of sharing data is perceived by most researchers more as a burden than as a chance to increase the visibility of their results and improve the value of their research. One of the main barriers to open research data (ORD) is the need for interoperable data e‐infrastructures that allow researchers to manage a whole scientific information life cycle and a variety of stakeholders from different sectors to retrieve and exploit these data. In the pilot project presented in this study an open access and open source repository was developed to store, preserve and make accessible heterogeneous agricultural ORD collected over decades of scientific research about plant‐microbe interactions, with a particular focus on plant virus disease symptoms. Additionally, a step‐by‐step installation guide to set up a repository and simple operating procedures for data stewardship were provided. 相似文献