Comprehensive survey of common bean viruses in Tanzania using next generation and Sanger sequencing techniques

Common bean (Phaseolus vulgaris L.) is an important legume crop in Tanzania and elsewhere in the tropics and subtropics. We employed a next-generation sequencing technique to detect viruses in common bean plant samples collected from five agricultural research zones in the country. The aim was to target and sequence virus-derived small RNAs. To achieve this, total RNA was isolated from dry leaf samples using the CTAB method. The CTAB buffer contained 2% CTAB, 100 mM Tris–HCl, 20 mM EDTA, 2.5 M NaCl, freshly prepared 1% sodium sulfite, 2% PVP and 2.5% 2-mercaptoethanol in nuclease-free water. Total RNA was sent to Fasteris in Switzerland where the small RNA was purified by electrophoresis in an acrylamide gel. The small RNA library was prepared using the Illumina TrueSeq small RNA  sample preparation kit (Illumina Inc., San Diego, CA, USA). Viruses were detected using VirusDetect software (v.1.6 and v.1.7) (available at http://bioinfo.bti.cornell.edu/cgi-bin/virusdetect/index.cgi) and supercomputer at CSC.fi. Viruses detected belonged to at least 11 genera.