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

Abstract

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.

Identification of Viruses Infecting Oats in Korea by Metatranscriptomics

“…However, a somewhat less-considered notion is that organisms also interact with a considerable diversity of viruses, designated the virome, which can be defined as virus-associated nucleic acids existing anywhere in plants, animals, or the environment. Recently, the generic detection and analyses of highly diverse viruses in a range of sample types have been performed using HTS as a platform offering an ideal and unique approach [40,41]. The ongoing reduction in the cost of HTS, along with improvement in the tools used for [39].…”

“…However, a somewhat less-considered notion is that organisms also interact with a considerable diversity of viruses, designated the virome, which can be defined as virus-associated nucleic acids existing anywhere in plants, animals, or the environment. Recently, the generic detection and analyses of highly diverse viruses in a range of sample types have been performed using HTS as a platform offering an ideal and unique approach [40,41]. The ongoing reduction in the cost of HTS, along with improvement in the tools used for HTS data analysis, are increasingly enabling researchers to address long-standing challenges, such as the identification of unknown viruses, the complexity of virus genomes, viral mutation, and virus replication, thereby providing unprecedented insights into plant viromes in a given environment [42][43][44].…”

Viruses of Economic Impact on Tomato Crops in Mexico: From Diagnosis to Management—A Review

“…PCR is the most used tool for the diagnosis of TYLCV, even though there are also tests based on rolling circle amplification (RCA), LAMP, and DNA hybridization [67,85]. As well as in other tomato viruses, NGS allows the identification and characterization of TYLCV isolates in infected plants [86]. Numerous serological techniques have been developed for the detection of this virus.…”

Risk perception associated with an emerging agri-food risk in Europe: plant viruses in agriculture

“…In Spain, Maize rough dwarf virus (MR) has been observed to infect 24% of commercial maize fields between 2001 and 2006, increasing to 80% in 2015 [ 18 ]. In Slovenia, Henbane Mosaic Virus (HMV) has been reported to significantly infect field tomatoes [ 19 ]. In Belgium, Pepino mosaic virus (PepMV) causes disease in tomato fruits and has been estimated to result in 50–60% of fruits being unmarketable [ 20 ] which significantly impacts the economic value of the crop [ 21 ].…”