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Abstract
A novel virus with distinct genome features was discovered by high throughput sequencing in a symptomatic blackcurrant plant. The virus, tentatively named Ribes americanum virus A (RAVA), has distinct genome organization and molecular features bridging genera in the order Tymovirales. The genome consists of 7106 nucleotides excluding the poly(A) tail. Five open reading frames were identified, with the first encoding a putative viral replicase with methyl transferase (MTR), AlkB, helicase, and RNA dependent RNA polymerase (RdRp) domains. The genome organization downstream of the replicase resembles that of members of the order Tymovirales with an unconventional triple gene block (TGB) movement protein arrangement with none of the other four putative proteins exhibiting significant homology to viral proteins. Phylogenetic analysis using replicase conserved motifs loosely placed RAVA within the Betaflexiviridae. Data strongly suggest that RAVA is a novel virus that should be classified as a species in a new genus in the Betaflexiviridae or a new family within the order Tymovirales.
Highlights
Technological developments in high throughput sequencing (HTS) have resulted in the rapid discovery and characterization of several novel plant viruses [1,2,3,4]
This study was initiated when an American blackcurrant maintained in the USDA-National ClonalGermplasm Repository (NCGR), Corvallis, Oregon (Ribes americanum; PI 617879) showed virus-like symptoms (Figure 1)
Alphaflexiviridae and Betaflexiviridae microscopy on tissue that was Because of the unique genome organization, we employed electron microscopy tested positive for the virus to determine whether a bacterial or fungal endophyte may be the cryptic of the the virus
Summary
Technological developments in high throughput sequencing (HTS) have resulted in the rapid discovery and characterization of several novel plant viruses [1,2,3,4]. Germplasm Repository (NCGR) maintains and distributes various accessions of specialty fruit and nut crop species from around the world [5]. This includes currant (Ribes spp.), a berry known for its potential health effects [6]. This study was initiated when an American blackcurrant maintained in the USDA-NCGR, Corvallis, Oregon (Ribes americanum; PI 617879) showed virus-like symptoms (Figure 1). The plant was infected with two viruses [3]: A waikavirus [7] and an undescribed virus in the order Tymovirales.
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