Global Advances in Tomato Virome Research: Current Status and the Impact of High-Throughput Sequencing

Viruses cause a big fraction of economically important diseases in major crops, including tomato. In the past decade (2011–2020), many emerging or re-emerging tomato-infecting viruses were reported worldwide. In this period, 45 novel viral species were identified in tomato, 14 of which were discovered using high-throughput sequencing (HTS). In this review, we first discuss the role of HTS in these discoveries and its general impact on tomato virome research. We observed that the rate of tomato virus discovery is accelerating in the past few years due to the use of HTS. However, the extent of the post-discovery characterization of viruses is lagging behind and is greater for economically devastating viruses, such as the recently emerged tomato brown rugose fruit virus. Moreover, many known viruses still cause significant economic damages to tomato production. The review of databases and literature revealed at least 312 virus, satellite virus, or viroid species (in 22 families and 39 genera) associated with tomato, which is likely the highest number recorded for any plant. Among those, here, we summarize the current knowledge on the biology, global distribution, and epidemiology of the most important species. Increasing knowledge on tomato virome and employment of HTS to also study viromes of surrounding wild plants and environmental samples are bringing new insights into the understanding of epidemiology and ecology of tomato-infecting viruses and can, in the future, facilitate virus disease forecasting and prevention of virus disease outbreaks in tomato

HIGH INFECTION PRESSURE OF ESFY PHYTOPLASMA THREATENS THE CULTIVATION OF STONE FRUIT SPECIES

European stone fruit yellows fi toplazma (ESFY; ‘Candidatus Phytoplasma prunorum’) povzroča pri koščičastih sadnih vrstah nevarno bolezen leptonekrozo koščičarjev. ESFY fi toplazma se na gostiteljske rastline iz roda Prunus prenaša z vektorjem češpljevo bolšico (Cacopsylla pruni), kakor tudi z vegetativnim razmnoževanjem. V nasadu koščičastih sadnih vrst, posajenem leta 2001 z brezvirusnim matičnim materialom, je bilo v letih 2004 – 2006 spremljano stanje glede okuženosti z ESFY fi toplazmo ter skupno odvzetih 158 vzorcev. Pri vseh sadnih vrstah so bila vzorčena tako simptomatična, kot asimptomatična drevesa. Od 15.7 % vzorčenih dreves marelic (Prunus armeniaca) v nasadu, je bila prisotnost fi toplazem potrjena pri 70.0 % vzorčenih drevesih. Pri slivah kitajsko- japonskega izvora (Prunus salicina) je bilo vzorčenje opravljeno pri tretjini matičnih rastlin, prisotnost ESFY fi toplazme je bila dokazana pri vseh vzorčenih rastlinah. Pri evropski slivi (Prunus domestica) je bila okuženost s fi toplazmami potrjena pri 51.0 % vzorčenih rastlin, pri čemer rastline večinoma niso kazale vidnih bolezenskih znamenj. Prisotnost ESFY fi toplazme je bila potrjena tudi pri 13.0 % vzorčenih drevesih breskve (Prunus persica). Pri češnji (Prunus avium) prisotnost fi toplazme ESFY ni bila potrjena. ESFY fi toplazma je bila v letu 2005 z laboratorijskim testiranjem potrjena tudi v vseh analiziranih vzorcih prenašalca Cacopsylla pruni.Stone fruit species are affected by severe disease caused by European stone fruit yellows phytoplasma (ESFY; ‘Candidatus Phytoplasma prunorum’). ESFY phytoplasma is transmitted to the host plants of Prunus spp. by the vector Cacopsylla pruni. The disease is graft-transmissible as well. The occurence of ESFY phytoplasma was monitored from 2004 to 2006 in a mother plant orchard of stone fruit species planted with virus free material in 2001 in the Primorska region of Slovenia. The total of 158 samples of mother plants were analysed in this period. The symptomatic and asymptomatic trees were analysed using molecular methods (PCR or nested-PCR). Among 15.7 % of sampled apricot trees (Prunus armeniaca) in the orchard, ESFY phytoplasma was detected in 70.0 % of samples. In the case of Japanese plum (Prunus salicina) samples were taken from one third of all Japanese plum trees and the presence of ESFY phytoplasma was confi rmed in all samples. In the European plum trees (Prunus domestica) the incidence of phytoplasma was determined in 51.0 % of sampled trees, where the plants in most cases did not show symptoms. ESFY phytoplasma was also detected in peaches and nectarines (Prunus persica) in 13.0 % of sampled trees while no detection of the phytoplasma was confi rmed in the samples of cherry trees (Prunus avium). With the survey performed in a mother plant orchard it was observed that especially young trees did not show typical symptoms and the infection was latent. In the year 2005, ESFY phytoplasma was detected in all tested samples of the vector Cacopsylla pruni captured in the vicinity of the mother plant orchard

HIGH INFECTION PRESSURE OF ESFY PHYTOPLASMA THREATENS THE CULTIVATION OF STONE FRUIT SPECIES

European stone fruit yellows fi toplazma (ESFY; ‘Candidatus Phytoplasma prunorum’) povzroča pri koščičastih sadnih vrstah nevarno bolezen leptonekrozo koščičarjev. ESFY fi toplazma se na gostiteljske rastline iz roda Prunus prenaša z vektorjem češpljevo bolšico (Cacopsylla pruni), kakor tudi z vegetativnim razmnoževanjem. V nasadu koščičastih sadnih vrst, posajenem leta 2001 z brezvirusnim matičnim materialom, je bilo v letih 2004 – 2006 spremljano stanje glede okuženosti z ESFY fi toplazmo ter skupno odvzetih 158 vzorcev. Pri vseh sadnih vrstah so bila vzorčena tako simptomatična, kot asimptomatična drevesa. Od 15.7 % vzorčenih dreves marelic (Prunus armeniaca) v nasadu, je bila prisotnost fi toplazem potrjena pri 70.0 % vzorčenih drevesih. Pri slivah kitajsko- japonskega izvora (Prunus salicina) je bilo vzorčenje opravljeno pri tretjini matičnih rastlin, prisotnost ESFY fi toplazme je bila dokazana pri vseh vzorčenih rastlinah. Pri evropski slivi (Prunus domestica) je bila okuženost s fi toplazmami potrjena pri 51.0 % vzorčenih rastlin, pri čemer rastline večinoma niso kazale vidnih bolezenskih znamenj. Prisotnost ESFY fi toplazme je bila potrjena tudi pri 13.0 % vzorčenih drevesih breskve (Prunus persica). Pri češnji (Prunus avium) prisotnost fi toplazme ESFY ni bila potrjena. ESFY fi toplazma je bila v letu 2005 z laboratorijskim testiranjem potrjena tudi v vseh analiziranih vzorcih prenašalca Cacopsylla pruni.Stone fruit species are affected by severe disease caused by European stone fruit yellows phytoplasma (ESFY; ‘Candidatus Phytoplasma prunorum’). ESFY phytoplasma is transmitted to the host plants of Prunus spp. by the vector Cacopsylla pruni. The disease is graft-transmissible as well. The occurence of ESFY phytoplasma was monitored from 2004 to 2006 in a mother plant orchard of stone fruit species planted with virus free material in 2001 in the Primorska region of Slovenia. The total of 158 samples of mother plants were analysed in this period. The symptomatic and asymptomatic trees were analysed using molecular methods (PCR or nested-PCR). Among 15.7 % of sampled apricot trees (Prunus armeniaca) in the orchard, ESFY phytoplasma was detected in 70.0 % of samples. In the case of Japanese plum (Prunus salicina) samples were taken from one third of all Japanese plum trees and the presence of ESFY phytoplasma was confi rmed in all samples. In the European plum trees (Prunus domestica) the incidence of phytoplasma was determined in 51.0 % of sampled trees, where the plants in most cases did not show symptoms. ESFY phytoplasma was also detected in peaches and nectarines (Prunus persica) in 13.0 % of sampled trees while no detection of the phytoplasma was confi rmed in the samples of cherry trees (Prunus avium). With the survey performed in a mother plant orchard it was observed that especially young trees did not show typical symptoms and the infection was latent. In the year 2005, ESFY phytoplasma was detected in all tested samples of the vector Cacopsylla pruni captured in the vicinity of the mother plant orchard

Tomato brown rugose fruit virus in aqueous environments – survival and significance of water-mediated transmission

Tomato brown rugose fruit virus (ToBRFV) has recently emerged as a major disease of tomatoes and peppers. ToBRFV is a seed- and contact-transmitted virus. In Slovenia, ToBRFV RNA was detected in samples of wastewater, river, and water used to irrigate plants. Even though the source of detected RNA could not be clearly established, this raised the question of the significance of the detection of ToBRFV in water samples and experimental studies were performed to address this question. The data presented here confirm that the release of virus particles from the roots of infected plants is a source of infectious ToBRFV particles in water and that the virus can remain infective up to four weeks in water stored at room temperature, while its RNA can be detected for much longer. These data also indicate that irrigation with ToBRFV-contaminated water can lead to plant infection. In addition, it has been shown that ToBRFV circulated in drain water in commercial tomato greenhouses from other European countries and that an outbreak of ToBRFV can be detected by regular monitoring of drain water. A simple method for concentrating ToBRFV from water samples and a comparison of the sensitivity of different methods, including the determination of the highest ToBRFV dilution still capable of infecting test plants, were also investigated. The results of our studies fill the knowledge gaps in the epidemiology and diagnosis of ToBRFV, by studying the role of water-mediated transmission, and provide a reliable risk assessment to identify critical points for monitoring and control

Host range and symptomatology of Pepino mosaic virus strains occurring in Europe

Pepino mosaic virus (PepMV) has caused great concern in the greenhouse tomato industry after it was found causing a new disease in tomato in 1999. The objective of this paper is to investigate alternative hosts and compare important biological characteristics of the three PepMV strains occurring in Europe when tested under different environmental conditions. To this end we compared the infectivity and symptom development of three, well characterized isolates belonging to three different PepMV strains, EU-tom, Ch2 and US1, by inoculating them on tomato, possible alternative host plants in the family Solanaceae and selected test plants. The inoculation experiments were done in 10 countries from south to north in Europe. The importance of alternative hosts among the solanaceous crops and the usefulness of test plants in the biological characterization of PepMV isolates are discussed. Our data for the three strains tested at 10 different European locations with both international and local cultivars showed that eggplant is an alternative host of PepMV. Sweet pepper is not an important host of PepMV, but potato can be infected when the right isolate is matched with a specific cultivar. Nicotiana occidentalis 37B is a useful indicator plant for PepMV studies, since it reacts with a different symptomatology to each one of the PepMV strains.Ravnikar, M.; Blystad, D.; Van Der Vlugt, R.; Alfaro Fernández, AO.; Del Carmen Cordoba, M.; Bese, G.; Hristova, D.... (2015). Host range and symptomatology of Pepino mosaic virus strains occurring in Europe. European Journal of Plant Pathology. 143(1):43-56. doi:10.1007/s10658-015-0664-1S43561431Alfaro-Fernández, A., Córdoba-Sellés, M. C., Herrera-Vásquez, J. A., Cebrián, M. C., & Jordá, C. (2009). Transmission of Pepino mosaic virus by the fungal vector Olpidium virulentus. Journal of Phytopathology, 158, 217–226.Charmichael, D. 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