Badnaviruses of Sweet Potato: Symptomless Coinhabitants on a Global Scale

Abstract

Sweet potato is among the most important root crops worldwide, particularly in developing countries, and its production is affected severely by a variety of virus diseases. During the last decade, a number of new viruses have been discovered in sweet potatoes through next-generation sequencing studies. Among them are viruses belonging to the genus Badnavirus and collectively assigned to the species sweet potato pakakuy virus (SPPV). We determined the complete genome sequence of two SPPV isolates and show the ubiquitous presence of similar viruses in germplasm and field material from around the globe. We show that SPPV is not integrated into the sweet potato genome, occurs only at extremely low titers, and is efficiently transmitted through seeds and cuttings. They are unaffected by virus elimination therapy and do not induce discernible symptoms in sweet potatoes or indicator host plants. They show considerable variation in their nucleotide sequences and correspond to several genetic lineages. Studies of their interaction with the two most important sweet potato viruses showed only limited synergistic increase in the titers of one of two SPPV isolates. We contend that these viruses may pose little threat to sweet potato production and more likely represent a new type of persistent virus in sweet potato.

Transcriptome analysis provides insights into the responses of sweet potato to sweet potato virus disease (SPVD)

“…The increase in SPFMV vsiRNAs at 12 wpi correlated with a reduced SPFMV transcript accumulation compared to 6 wpi indicated an increase in RNA silencing-mediated control of virus replication at later stages of the infection. The increased SPFMV vsiRNA levels found at 12 wpi is comparable, though far less extreme to what has been found in previous studies with cultivar ‘Huachano’ ( Cuellar et al, 2015 ; Kreuze et al, 2009 , 2020 ), and may thus be a general outcome of prolonged infection with SPFMV and SPCSV in susceptible cultivars. A significant change from 22- to 21-nt SPFMV-derived siRNAs observed in coinfected plants compared to singly infected plants might be related to failure of RNA silencing mediated control of SPFMV as it was correlated with increased SPFMV transcripts.…”

Identification of Cacao Mild Mosaic Virus (CaMMV) and Cacao Yellow Vein-Banding Virus (CYVBV) in Cocoa (Theobroma cacao) Germplasm

“…In addition, it is relevant to note that the occurrence of viruses that do not induce disease symptoms are known in several other crops. For example, the examination of sweet potato germplasm from around the globe has revealed the widespread presence of the badnavirus sweet potato pakakuy virus (SPPV) [34]. This virus, which only occurs at very low titres, is efficiently transmitted through seeds and cuttings and does not induce any obvious symptoms in either sweet potatoes or indicator plants.…”

A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses

“…For example, the viral sequences detected may correspond to a bona fide virus infecting other organisms associated with the sample, including bacteria, fungi, or arthropods [ 122 , 123 ] or to viral sequences integrated into the plant genome [ 124 , 125 ]. As stated previously [ 125 ], relevant scientific expertise is essential for sound biological interpretation of HTS results, in particular when identifying a target with a low titer, a poorly characterized species, an uncharacterized organism, or sequences integrated in the host genome [ 6 , 126 ]. In this latter case, careful phylogenetic analysis, including retrotransposons and viruses reported only from integration events in plant genomes [ 91 , 92 , 93 ] may provide critical information on whether the sequences identified correspond to an autonomously replicating (episomal) virus or to cellular transcripts from integrated viral elements.…”