Abstract
Limited studies have been undertaken with regard to virus complexes contributing to the aetiology of sweet potato virus disease (SPVD) in South Africa (SA). In this study, a metagenomic approach was adopted to reveal the genetic diversity of viruses infecting sweet potato. In order to undertake a comprehensive analysis of viral sequences, total RNA was isolated from 17 asymptomatic and symptomatic sweet potato plants that were collected from the Eastern (EC) and Western Cape (WC) provinces of SA. DNase-treated total RNA was depleted of ribosomal RNA (rRNA) and deep-sequenced using the Illumina MiSeq platform. Genomic DNA, isolated from the same plants, underwent rolling circle amplification (RCA) and deep sequencing. Sequence reads were analysed with the CLC Bio Genomics Workbench. Both de novo and reference-guided assemblies were performed resulting in four near full-length RNA virus genomes. BLAST searches using de novo assembled sequences against published virus genomes confirmed the presence of previously detected begomoviruses in the Western Cape (WC) province, namely Sweet potato mosaic virus (SPMaV) and Sweet potato leaf curl Sao Paulo virus (SPLCSPV). The begomoviruses were detected in mixed infections with two major disease-causing RNA viruses, Sweet potato feathery mottle virus (SPFMV) and Sweet potato chlorotic stunt virus (SPCSV). The sequence data further demonstrated mixed infections of RNA and DNA viruses from 11 of the 17 sequenced samples. Metagenomics is a reliable diagnostic tool for virus diversity detection, in particular virus-complexes and synergies affecting disease aetiology.
Highlights
Sweet potato (Ipomoea batatas (L.) Lam.) is a dicotyledonous perennial plant belonging to the morning glory family Convolvulaceae
The most severe symptoms were observed on sample KF1, which was collected from the Western Cape (WC) province
The phenotypic data suggests that sweet potato viruses were more prevalent in the WC, since most of the samples collected from this province were symptomatic
Summary
Sweet potato (Ipomoea batatas (L.) Lam.) is a dicotyledonous perennial plant belonging to the morning glory family Convolvulaceae. It produces edible, highly nutritious tubers and is ranked as the 3rd most important root crop and the 7th most important staple crop in the world (Valverde et al, 2007; Clark et al, 2012). Sweet potato is an attractive crop to resource-poor farmers as it is easy to grow, high yielding, is drought and heat tolerant, and crowds out weeds (Kays, 2004). It has been recorded that viral diseases can decrease yield and quality of sweet potato storage roots by 30–100% in countries such as the United States (Valverde et al, 2007), Peru (Cuellar et al, 2008), SA (Domola et al, 2008), Kenya (Ateka et al, 2004) and Ethiopia (Tesfaye et al, 2011)
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