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

Correction: Haegeman et al. Looking beyond Virus Detection in RNA Sequencing Data: Lessons Learned from a Community-Based Effort to Detect Cellular Plant Pathogens and Pests. Plants 2023, 12, 2139.

In the original publication [...]

Looking beyond Virus Detection in RNA Sequencing Data: Lessons Learned from a Community-Based Effort to Detect Cellular Plant Pathogens and Pests.

High-throughput sequencing (HTS), more specifically RNA sequencing of plant tissues, has become an indispensable tool for plant virologists to detect and identify plant viruses. During the data analysis step, plant virologists typically compare the obtained sequences to reference virus databases. In this way, they are neglecting sequences without homologies to viruses, which usually represent the majority of sequencing reads. We hypothesized that traces of other pathogens might be detected in this unused sequence data. In the present study, our goal was to investigate whether total RNA-seq data, as generated for plant virus detection, is also suitable for the detection of other plant pathogens and pests. As proof of concept, we first analyzed RNA-seq datasets of plant materials with confirmed infections by cellular pathogens in order to check whether these non-viral pathogens could be easily detected in the data. Next, we set up a community effort to re-analyze existing Illumina RNA-seq datasets used for virus detection to check for the potential presence of non-viral pathogens or pests. In total, 101 datasets from 15 participants derived from 51 different plant species were re-analyzed, of which 37 were selected for subsequent in-depth analyses. In 29 of the 37 selected samples (78%), we found convincing traces of non-viral plant pathogens or pests. The organisms most frequently detected in this way were fungi (15/37 datasets), followed by insects (13/37) and mites (9/37). The presence of some of the detected pathogens was confirmed by independent (q)PCRs analyses. After communicating the results, 6 out of the 15 participants indicated that they were unaware of the possible presence of these pathogens in their sample(s). All participants indicated that they would broaden the scope of their bioinformatic analyses in future studies and thus check for the presence of non-viral pathogens. In conclusion, we show that it is possible to detect non-viral pathogens or pests from total RNA-seq datasets, in this case primarily fungi, insects, and mites. With this study, we hope to raise awareness among plant virologists that their data might be useful for fellow plant pathologists in other disciplines (mycology, entomology, bacteriology) as well

Looking beyond Virus Detection in RNA Sequencing Data: Lessons Learned from a Community-Based Effort to Detect Cellular Plant Pathogens and Pests.

peer reviewedHigh-throughput sequencing (HTS), more specifically RNA sequencing of plant tissues, has become an indispensable tool for plant virologists to detect and identify plant viruses. During the data analysis step, plant virologists typically compare the obtained sequences to reference virus databases. In this way, they are neglecting sequences without homologies to viruses, which usually represent the majority of sequencing reads. We hypothesized that traces of other pathogens might be detected in this unused sequence data. In the present study, our goal was to investigate whether total RNA-seq data, as generated for plant virus detection, is also suitable for the detection of other plant pathogens and pests. As proof of concept, we first analyzed RNA-seq datasets of plant materials with confirmed infections by cellular pathogens in order to check whether these non-viral pathogens could be easily detected in the data. Next, we set up a community effort to re-analyze existing Illumina RNA-seq datasets used for virus detection to check for the potential presence of non-viral pathogens or pests. In total, 101 datasets from 15 participants derived from 51 different plant species were re-analyzed, of which 37 were selected for subsequent in-depth analyses. In 29 of the 37 selected samples (78%), we found convincing traces of non-viral plant pathogens or pests. The organisms most frequently detected in this way were fungi (15/37 datasets), followed by insects (13/37) and mites (9/37). The presence of some of the detected pathogens was confirmed by independent (q)PCRs analyses. After communicating the results, 6 out of the 15 participants indicated that they were unaware of the possible presence of these pathogens in their sample(s). All participants indicated that they would broaden the scope of their bioinformatic analyses in future studies and thus check for the presence of non-viral pathogens. In conclusion, we show that it is possible to detect non-viral pathogens or pests from total RNA-seq datasets, in this case primarily fungi, insects, and mites. With this study, we hope to raise awareness among plant virologists that their data might be useful for fellow plant pathologists in other disciplines (mycology, entomology, bacteriology) as well.Plant Health Bioinformatics Networ

Correction: Haegeman et al. Looking beyond Virus Detection in RNA Sequencing Data: Lessons Learned from a Community-Based Effort to Detect Cellular Plant Pathogens and Pests. <i>Plants</i> 2023, <i>12</i>, 2139

In the original publication [...