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

Mark Paul Selda Rivarez,Ana Vučurović,Denis Kutnjak,Nataša Mehle,Maja Ravnikar

doi:10.3389/fmicb.2021.671925

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.

Highlights

Tomato (Solanum lycopersicum L.) is one of the most economically valuable fruit or vegetable crops worldwide, valued at 93.9 billion US dollars in 2018, with yield estimated at 180.8 million tons in 2019 (FAOSTAT, 2020)
In the second part of this review, we focus on important tomato viruses, which caused significant economic losses in tomato production in the past decade and new virus discoveries in tomato, for which limited or no knowledge about potential impact on tomato health is available
New discoveries and studies on emergence of tomato viruses in the recent decade contributed to our understanding of the tomato virome, its diversity, virus ecology, and epidemiology

Summary

Introduction

Tomato (Solanum lycopersicum L.) is one of the most economically valuable fruit or vegetable crops worldwide, valued at 93.9 billion US dollars in 2018, with yield estimated at 180.8 million tons in 2019 (FAOSTAT, 2020). Review of the past and recent discoveries of viruses in tomato shows that tomato is currently associated with at least 312 different viral species, which is likely, according to our knowledge, the largest recorded number known for any cultivated plant. E.g., for majority (>60%) of the HTS-based new virus discoveries, whole genome sequence was determined, primers for detection of the virus with PCR were designed, local survey of prevalence was done, and co-infection with other viruses was checked (Figure 2A).

Results

Conclusion