Hybrid RNA sequencing of broad bean wilt virus 2 from faba beans

High-throughput sequencing (HTS) is an important tool for plant virus detection and discovery. HTS technologies such as Nanopore sequencing has been rapidly developing in recent years, and offers new possibilities for fast routine diagnostic applications. This study compared MiSeq (Illumina) RNA-Seq with the MinION sequencer (Oxford Nanopore Technologies) (ONT) direct-RNA-Seq methods to detect and sequence the broad bean wilt virus 2 (BBWV2) genome. The Illumina BBWV2 RNA1 and RNA2 genome segments were intact and matched with ONT with 99.1% and 98.8% nucleotide identity (nt) match, respectively. The RNA1 genome derived from ONT had deletions within the nucleoside-triphosphate binding and protease factor open-reading frames, and the upstream of five untranslated regions. However, its RNA2 was intact, and no sequencing errors were observed. The ONT and Illumina RNA1 and RNA 2 BBWV2 genome segments clustered together phylogenetically along with other none-Fabaceae species, BBWV2 RNA1 NCBI accession KC790225, and RNA 2 MW556592 both from China. This is the first BBWV2 genome study reported in Australia and forms part of the strategy to integrate versatile diagnostic genomics tools at the border to safeguard the Australian grains industry.