Detection of RNA viruses in Solanum quitoense by high-throughput sequencing (HTS) using total and double stranded RNA inputs

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

“…However, no studies have been reported identifying wheat-infecting viruses in Korea; therefore, we aimed to determine the composition of the wheat virome by utilizing field samples from three major domestic wheat-producing regions through two HTS platforms. The HTS platform is considered one of the most exciting technologies for plant virus diagnostics in integrated disease management programs, as it facilitates the highly sensitive identification and characterization of viruses [ 39 ]. Previous studies using HTS revealed the infection of novel viruses in wheat, such as wheat virus Q, wheat yellow stunt-associated betaflexivirus, and the first umbra-like associated RNA viruses named wheat umbra-like virus [ 32 , 34 , 35 ].…”

Detection of RNA viruses in potato seed-tubers from northern Antioquia (Colombia)

“…Phylogenetic analysis of scaffolds and/or contigs revealed the phylogenetic affinity of the viruses detected by RNAseq with previously known isolates in Colombia. For PLRV, sequences from both certified (BST19) and uncertified (BST20) S. tuberosum seed-tubers were part of the main clade found for this virus worldwide (Guyader & Ducray, 2002;, and closely related to isolate M1 obtained from S. quitoense in Antioquia by Gallo et al (2021a). Analysis of the PMTV RNA3 scaffold obtained from the uncertified S. tuberosum seed-lots (BST20) formed an independent clade between isolates of worldwide distribution (Gil et al, 2011;, and local isolates infecting S. tuberosum (CO2 and CO1) or P. peruviana (M7 and M2) recently reported by Gallo et al (2020) (Figure 3).…”