Small RNA deep sequencing‐based detection and further evidence of DNA viruses infecting sweetpotato plants in Tanzania

Abstract

Small interfering RNA deep sequencing (SRDS) was used to detect viruses in 23 sweetpotato plants, collected from various locations in Tanzania. Alignment of small RNA reads using a MAQ program recovered genomes of viruses from five families, namely Geminiviridae (2), Closteroviridae (1), Betaflexiviridae (1), Caulimoviridae (1) and Potyviridae (1). This was in agreement with the variation of symptoms observed on sweetpotato plants in fields and screen house, which included leaf curl, vein yellowing, chlorosis, stunted growth and brown blotches. PCR was also used to confirm the occurrence of viruses associated with leaf curl and symptomless infections. A complete genome (2768 nucleotides) was obtained for a sweepovirus that was 89.9% identical to the strain of Sweet potato leaf curl Sao Paulo virus (SPLCSPV; Begomovirus) reported in South Africa. Sweepoviruses are known to undergo frequent recombinations and evidence for this was found in the SPLCSPV sequence studied. The SRDS-based results indicated occurrence of the poorly studied Sweet potato badnavirus B (SPBV-B) and Sweet potato badnavirus A (collectively known as Sweet potato pakakuy virus; SPPV; Caulimoviridae) in sweetpotato plants in Tanzania. A 5 -end partial sequence (3065 nucleotides), encoding hypothetical, movement and coat proteins, was obtained and found to be 86.3% and 73.1% identical to SPBV-B and SPBV-A, respectively. A survey for the distribution of SPPV and Sweet potato symptomless mastrevirus 1 (SPSMV-1) showed that these viruses were wide spread and co-infecting sweetpotato plants in Tanzania. The importance of East Africa as a hot spot for the diversity and evolution of sweet potato viruses is discussed.

Viruses infecting common bean (Phaseolus vulgaris L.) in Tanzania: A review on molecular characterization, detection and disease management options

“…These methods are robust in detection of plant viruses from different families and have led to discovery of novel plant viruses (Adams et al, 2009;Kreuze et al, 2009;Boonham et al, 2014;Zheng et al, 2017). Some studies conducted in or using plant samples from Tanzania have employed NGS to detect plant viruses but not those infecting common bean (Mbanzibwa et al, 2014;Ndunguru et al, 2015). Elsewhere, viruses infecting common bean have been detected and sequenced using NGS (Kehoe et al, 2014;Maina et al, 2016).…”

“…In detection of plant viruses infecting crops other than common bean in Tanzania, either sequencing was done on viral small RNAs, naturally generated by plants as they defend against invading viruses, or on intact RNA (Mlotshwa et al, 2008;Mbanzibwa et al, 2014;Ndunguru et al, 2015). The NGS studies on Tanzanian plant RNA samples enabled detection of viruses not previously known to occur in sweet potato (Mbanzibwa et al, 2014) and the sequencing of complete genomes of Cassava brown streak virus (Ipomovirus) and Ugandan cassava brown streak virus (Ipomovirus), and hence studies on evolution of these viruses (Ndunguru et al, 2015). Following generation of information on these viruses, plant breeders have targeted specific species in their breeding programmes and have diagnostic tools to confirm viruses with which they challenge their breeding materials.…”

Invertebrate pests and diseases of sweetpotato (Ipomoea batatas): a review and identification of research priorities for smallholder production

“…In some areas sweetpotato viruses are a major constraint, often reducing yield by more 50% and up to 90% (Carey et al, 1999;Gutiérrez et al, 2003;Gibson et al, 2004;Valverde et al, 2007;Davis & Ruabete, 2010;Wang et al, 2010;Okpul et al, 2011;Clark et al, 2012;Cuellar et al, 2015;Gibson & Kreuze, 2015). The most common form of spread of viruses is through propagation material, in which a taxonomically diverse range of viruses can be present (Clark & Moyer, 1988;Moyer & Larsen, 1991;Gibson et al, 1997;Mbanzibwa et al, 2014). Some viruses are vectored by aphids and whitefly Clark et al, 2012).…”

“…This impact on vegetative growth greatly reduces yield potential (Wang et al, 2010). Other symptoms include leaf curl, brown blotches, yellowing in the veins, chlorosis of the leaves and in serious cases, stunted growth (Mbanzibwa et al, 2014). Viruses can also cause 'russet crack', necrotic lesions or corking on the storage root (Ames et al, 1996).…”

Occurrence and genetic variability of partial coat protein gene of Sweet potato leaf curl virus (SPLCV) in Kenya

“…This could be due to its universal broad detection (Li et al, 2013). The presence of SPLCV in Taita Taveta could be attributed to cross-border trade with Tanzania where begomoviruses have been recently reported (Mbanzibwa et al, 2014). The Central region had the least SPLCV incidence.…”