Determination of the grapevine virome by high-throughput sequencing and grapevine viruses detection in Serra Gaúcha, Brazil

Abstract

Among grapevine (Vitis spp.) pathogens, viruses stand out, considering that this fruit plant is broadly susceptible to them and that they cause several diseases, reducing quality and yield of grape production. However, detecting and identifying viral infections in grapevines can be challenging. The objectives of this study were to detect grapevine viral pathogens by high-throughput sequencing (HTS) and identify grapevine viruses associated with plant propagation material from different origins. A comprehensive picture of a vine exhibiting virus-related symptoms was generated. The detected virome included four different pathogens and their variants. In addition, the incidence of seven viral pathogens was determined in samples collected in three vineyards of the main grape-growing region of Brazil. It is suggested that the observed infections could be related to the technological level of the production system adopted by these grape growers.

Analysis of virome by high-throughput sequencing disclosed multiple infection in a single grapevine plant

“…According to these authors, disease itself is triggered by the really damaging viral species that disrupt the constitution of the natural virome in the plant. In fact, previous reports with samples of grapevines collected in Brazil usually detected grSPaV, hSVd and/ or gYSVd-1 and another virus that was actually implicated in the pathology of the viral disease, for example, glraV-3 as determined by FAjArDO et al (2020). In the present research, gVB stands out in the virome determined by hTS.…”

Virome Status of Preclonal Candidates of Grapevine Varieties (Vitis vinifera L.) From the Slovenian Wine-Growing Region Primorska as Determined by High-Throughput Sequencing

“…Most methods for detection and identification require prior knowledge of the potential pathogens (e.g., use of antibodies in serological methods or virus specific primers in PCR amplification), with the exception of the metagenomic approach called high-throughput sequencing technology (HTS). HTS is a powerful technology that enables rapid detection of viral entities in plant tissues, including unknown as well as known viruses and viroids in symptomatic and asymptomatic plants, without the need for prior knowledge ( Al Rwahnih et al, 2009 ; Kreuze et al, 2009 ; Fajardo et al, 2020 ). HTS of small RNAs (small RNA sequencing; sRNA-seq) has been shown to be efficient in detecting plant viruses or viroids ( Kreuze et al, 2009 ; Kashif et al, 2012 ; Vives et al, 2013 ; Jakse et al, 2015 ; Singh et al, 2020 ).…”

Analysis of Wheat Virome in Korea Using Illumina and Oxford Nanopore Sequencing Platforms

“…The limitations can be overcome by high-throughput sequencing (HTS) techniques combined with metagenomic analysis. HTS is a very powerful technology to accurately identify viral entities in plant samples, including viruses and viroids in symptomatic as well as asymptomatic plants without any prior knowledge [ 18 , 19 ]. HTS approaches have been utilized for discovery, diagnostic, and evolutionary studies over the past two decades.…”