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Global advances in tomato virome research: current status and the impact of high-throughput sequencing

Rivarez MPS, Vučurović A, Mehle N, Ravnikar M and Kutnjak D (2021) Global Advances in Tomato Virome Research: Current Status and the Impact of High-Throughput Sequencing. Front. Microbiol. 12:671925. doi: 10.3389/fmicb.2021.671925 In this review paper we have collected the existing knowledge about the viruses infecting tomato, focusing on the viruses that caused important economic damage in tomato production in a past decade. We have also addressed how high-throughput sequencing technologies have contributed to discovery of novel viruses infecting tomato and evaluated the extent of post-discovery characterisation studies for such viruses.

Viruses cause a big fraction of economically important diseases in major crops, including tomato. In the past decade (2011–2020) 45 novel viral species were identified in tomato, 14 of which were discovered using high-throughput sequencing (HTS). 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. The review of databases and literature revealed at least 312 virus, satellite virus, or viroid species associated with tomato, which is likely the highest number recorded for any plant. 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. 

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