Detección por hibridación molecular de virus en cultivos de tomate con manejo convencional, integrado y ecológico

[ES] Los virus causan graves daños y pérdidas económicas en cultivos de tomate de todo el mundo, lo que supone una reducción en la producción. Entre los virus más importantes están los virus del mosaico del tomate (ToMV), del mosaico del pepino (CMV), del bronceado del tomate (TSWV), del mosaico del pepino dulce (PepMV), del moteado de la parietaria (PMoV) y del rizado amarillo del tomate (TYLCV). Resulta crucial disponer de un método de detección preciso y rápido para evaluar la incidencia de estos virus y aplicarlos en métodos de control de la enfermedad. En este trabajo se puso a punto la hibridación molecular para detectar estos virus y se aplicó para estimar como varía la incidencia de los mismos durante el cultivo de tomate en campos con un manejo convencional, integrado y ecológico.[EN] The growing interest in carrying out sustainable practices with the environment has also come to agriculture, resulting in an increase on the ecological or organic practices in the last decades. The viral diseases cause serious damage and economical loses in tomato crops all over the world, which is translated into a reduction of the production. Among the most important viruses is it possible to find the Tomato Mosaic Virus (ToMV), the Cucumber Mosaic Virus (CMV), the Tomato Spotted Wilt Virus (TSWV), the Pepino Mosaic Virus (PepMV), the Parietaria Mottle Virus (PMoV) or the Tomato Yellow Leaf Curl Virus (TYLCV). It is crucial to have a precise and fast detection method, in order to evaluate the incidence of these viruses and to apply the most suitable control methods for the disease. In this project, the molecular hybridization has been set-up for detecting these viruses, and has been applied to analyze the variations on the viral incidence during the tomato crop in fields under conventional, integrated and organic managements.Salavert Pamblanco, F. (2016). Detección por hibridación molecular de virus en cultivos de tomate con manejo convencional, integrado y ecológico. http://hdl.handle.net/10251/68728.TFG

The opium poppy in Europe: exploring its origin and dispersal during the Neolithic

A new project aims to define the origins and dispersal patterns of the opium poppy in Neolithic Western Europe through a comprehensive programme of radiocarbon dating

Cucurbit chlorotic yellows virus p22 suppressor of RNA silencing binds single-, double-stranded long and short interfering RNA molecules in vitro

[EN] Cucurbit chlorotic yellows virus (CCYV) is a new member of the genus Crinivirus (family Closteroviridae) with a bi-partite genome. CCYV RNA 1-encoded p22 has recently been reported to be a weak local suppressor of RNA silencing for which an interaction with cucumber SKP1LB1 through an F-box-like motif was demonstrated to be essential. Using a bacterially expressed maltose-binding protein (MBP) fusion of CCYV p22 in electrophoretic mobility shift assays (EMSA), we have examined in vitro its ability to bind different RNA templates. Our experiments showed that CCYV p22 is able to bind to ss and ds long RNAs, in addition to ss and ds small interfering (si) RNA molecules. CCYV p22 deletion mutants (MBP_CCYV DEL1-4) were produced that covered the entire protein, with MBP_CCYV DEL2 corresponding to the F-box motif and its flanking sequences. None of these deletions abolished the capacity of CCYV p22 to bind ss- and dsRNA molecules. However, deletions affecting the C-terminal half of the protein resulted in decreased binding efficiency for either ss- or dsRNA molecules indicating that essential elements for these interactions are located in this region. Taken together, our data add to current knowledge of the mode of action of suppressors of RNA silencing encoded by genes sited at the 3'-terminus of crinivirus genomic RNA 1, and shed light on the involvement of CCYV p22 in the suppression of RNA silencing and/or in another role in the virus life cycle via RNA binding.Salavert, F.; Navarro Bohigues, JA.; Owen, CA.; Khechmar, S.; Pallás Benet, V.; Livieratos, IC. (2020). Cucurbit chlorotic yellows virus p22 suppressor of RNA silencing binds single-, double-stranded long and short interfering RNA molecules in vitro. Virus Research. 279:1-8. https://doi.org/10.1016/j.virusres.2020.197887S18279Abrahamian, P. E., Seblani, R., Sobh, H., & Abou-Jawdah, Y. (2013). 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Virology, 379(1), 168-174. doi:10.1016/j.virol.2008.06.020Chen, S., Sun, X., Shi, Y., Wei, Y., Han, X., Li, H., … Shi, Y. (2019). Cucurbit Chlorotic Yellows Virus p22 Protein Interacts with Cucumber SKP1LB1 and Its F-Box-Like Motif Is Crucial for Silencing Suppressor Activity. Viruses, 11(9), 818. doi:10.3390/v11090818Cuellar, W. J., Tairo, F., Kreuze, J. F., & Valkonen, J. P. T. (2008). Analysis of gene content in sweet potato chlorotic stunt virus RNA1 reveals the presence of the p22 RNA silencing suppressor in only a few isolates: implications for viral evolution and synergism. Journal of General Virology, 89(2), 573-582. doi:10.1099/vir.0.83471-0Cuellar, W. J., Kreuze, J. F., Rajamaki, M.-L., Cruzado, K. R., Untiveros, M., & Valkonen, J. P. T. (2009). Elimination of antiviral defense by viral RNase III. Proceedings of the National Academy of Sciences, 106(25), 10354-10358. doi:10.1073/pnas.0806042106GYOUTOKU, Y., OKAZAKI, S., FURUTA, A., ETOH, T., MIZOBE, M., KUNO, K., … OKUDA, M. (2009). Chlorotic yellows disease of melon caused by Cucurbit chlorotic yellows virus, a new crinivirus. Japanese Journal of Phytopathology, 75(2), 109-111. doi:10.3186/jjphytopath.75.109Herranz, M. C., & Pallás, V. (2004). RNA-binding properties and mapping of the RNA-binding domain from the movement protein of Prunus necrotic ringspot virus. Journal of General Virology, 85(3), 761-768. doi:10.1099/vir.0.19534-0Huang, L.-H., Tseng, H.-H., Li, J.-T., & Chen, T.-C. (2010). First Report of Cucurbit chlorotic yellows virus Infecting Cucurbits in Taiwan. Plant Disease, 94(9), 1168-1168. doi:10.1094/pdis-94-9-1168bKataya, A. R. A., Suliman, M. N. S., Kalantidis, K., & Livieratos, I. C. (2009). Cucurbit yellow stunting disorder virus p25 is a suppressor of post-transcriptional gene silencing. Virus Research, 145(1), 48-53. doi:10.1016/j.virusres.2009.06.010Klaassen, V. A., Mayhew, D., Fisher, D., & Falk, B. W. (1996). In VitroTranscripts from Cloned cDNAs of the Lettuce Infectious Yellows Closterovirus Bipartite Genomic RNAs Are Competent for Replication inNicotiana benthamianaProtoplasts. Virology, 222(1), 169-175. doi:10.1006/viro.1996.0407Kreuze, J. F., Savenkov, E. I., Cuellar, W., Li, X., & Valkonen, J. P. T. (2005). Viral Class 1 RNase III Involved in Suppression of RNA Silencing. Journal of Virology, 79(11), 7227-7238. doi:10.1128/jvi.79.11.7227-7238.2005Kubota, K., & Ng, J. C. K. (2016). Lettuce chlorosis virus P23 Suppresses RNA Silencing and Induces Local Necrosis with Increased Severity at Raised Temperatures. Phytopathology®, 106(6), 653-662. doi:10.1094/phyto-09-15-0219-rLandeo-Ríos, Y., Navas-Castillo, J., Moriones, E., & Cañizares, M. C. (2016). The p22 RNA silencing suppressor of the crinivirus Tomato chlorosis virus preferentially binds long dsRNAs preventing them from cleavage. Virology, 488, 129-136. doi:10.1016/j.virol.2015.11.008Marcos, J. F., Vilar, M., Pérez-Payá, E., & Pallás, V. (1999). In VivoDetection, RNA-Binding Properties and Characterization of the RNA-Binding Domain of the p7 Putative Movement Protein from Carnation Mottle Carmovirus (CarMV). Virology, 255(2), 354-365. doi:10.1006/viro.1998.9596Mashiko, T., Wang, W.-Q., Hartono, S., Suastica, G., Neriya, Y., Nishigawa, H., & Natsuaki, T. (2019). The p27 open reading frame of tomato infectious chlorosis virus encodes a suppressor of RNA silencing. Journal of General Plant Pathology, 85(4), 301-305. doi:10.1007/s10327-019-00850-0Navarro, J. A., Genovés, A., Climent, J., Saurí, A., Martínez-Gil, L., Mingarro, I., & Pallás, V. (2006). RNA-binding properties and membrane insertion of Melon necrotic spot virus (MNSV) double gene block movement proteins. Virology, 356(1-2), 57-67. doi:10.1016/j.virol.2006.07.040Okuda, M., Okazaki, S., Yamasaki, S., Okuda, S., & Sugiyama, M. (2010). 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Managing the deluge of newly discovered plant viruses and viroids: an optimized scientific and regulatory framework for their characterization and risk analysis

The advances in high-throughput sequencing (HTS) technologies and bioinformatic tools have provided new opportunities for virus and viroid discovery and diagnostics. Hence, new sequences of viral origin are being discovered and published at a previously unseen rate. Therefore, a collective effort was undertaken to write and propose a framework for prioritizing the biological characterization steps needed after discovering a new plant virus to evaluate its impact at different levels. Even though the proposed approach was widely used, a revision of these guidelines was prepared to consider virus discovery and characterization trends and integrate novel approaches and tools recently published or under development. This updated framework is more adapted to the current rate of virus discovery and provides an improved prioritization for filling knowledge and data gaps. It consists of four distinct steps adapted to include a multi-stakeholder feedback loop. Key improvements include better prioritization and organization of the various steps, earlier data sharing among researchers and involved stakeholders, public database screening, and exploitation of genomic information to predict biological properties

Chronological framework of the origin and early dispersal of Opium Poppy in Europe

International audienc

The origin and early dispersal of opium poppy (Papaver somniferum l.) in western Europe

International audienc

The origin and early dispersal of opium poppy (Papaver somniferum l.) in western Europe

International audienc

Exploring the long-term interaction of the opium poppy and past human societies: first results from the archaeological database and contribution of morphometric and genetic analyses

The opium poppy (Papaver somniferum) is a multi-purposes plant used for food (oil, dry seeds), in pharmaceutical or narcotic products and as an ornamental plant. Nevertheless, its history is still largely unknown, notably because of its imprecise phylogeny, the difficulty of the recovering of seed on archaeological sites, or the absence of identified morphological traits of domestication. A co-funded research project (ANR JcJc Poppy, FCT Dope) aims to unravel the origin of the plant, the complexity of its domestication process, their dispersal trajectories and its past uses using archaeological and genetic information (https://opiumpoppy.hypotheses.org/).To date, first reliable chronological landmarks were established thanks to radiocarbon dating performed with the compact AMS EchoMicadas directly on archaeological opium poppy remains. The opium poppy is present in central Italy from the middle of the 6th millennium in the heart of the region supposed to shelter its wild ancestor. Nevertheless, the majority of the earliest sites that have yielded seeds are located in temperate Europe as early as 5300 BCE, raising questions about the modalities (vectors, status) of the plant's diffusion between the first two major agro-pastoral systems of Western Europe (Salavert et al., 2020). Was the plant unintentionally disseminated with the status of crop weed, or was it already cultivated, and if so, for what purpose(s)? Initially, the aim will be to exploit an ongoing database listing the attestations of opium poppy between 6000 and 50 BCE in Europe, the Near East and North Africa. The critical analysis of the chronological attribution of the remains, and of the archaeological contexts will allow to propose preliminary research path to answer those questions. These results will then be discussed in the light of morphometric-geometric analyses of archaeological seeds (Jesus et al., 2021) and genetic analyses of current and sub-actual opium poppy varieties in order to explore the long-term interaction of the opium poppy and past human societies through a crossdisciplinary strategy

Was Papaver somniferum a cultivated wild plant in Neolithic Europe? First results of the application of geometric morphometrics to distinguish between wild and domestic seeds

International audienc

Managing the deluge of newly discovered plant viruses and viroids

The advances in high-throughput sequencing (HTS) technologies and bioinformatic tools have provided new opportunities for virus and viroid discovery and diagnostics. Hence, new sequences of viral origin are being discovered and published at a previously unseen rate. Therefore, a collective effort was undertaken to write and propose a framework for prioritizing the biological characterization steps needed after discovering a new plant virus to evaluate its impact at different levels. Even though the proposed approach was widely used, a revision of these guidelines was prepared to consider virus discovery and characterization trends and integrate novel approaches and tools recently published or under development. This updated framework is more adapted to the current rate of virus discovery and provides an improved prioritization for filling knowledge and data gaps. It consists of four distinct steps adapted to include a multi-stakeholder feedback loop. Key improvements include better prioritization and organization of the various steps, earlier data sharing among researchers and involved stakeholders, public database screening, and exploitation of genomic information to predict biological properties