The main pulse legume crops grown in Australia are chickpea (Cicer arietinum), lupin (Lupinus angustifolius, L. albus), faba bean (Vicia faba), field pea (Pisum sativum), lentil (Lens culinaris) and mung bean (Vigna radiata). The main viruses infecting pulse crops include the Poleroviruses; Turnip yellows virus (TuYV) and Phasey bean mild yellow virus (PBMYV), the Luteoviruses; Soybean dwarf virus (SbDV) and Bean Leafroll virus (BLRV), the Alfamovirus; Alfalfa mosaic virus (AMV), the Cucumovirus; Cucumber mosaic virus (CMV) and the Potyvirus, Bean yellow mosaic virus (BYMV). For many pulse crops the Luteoviridae viruses (includes Poleroviruses and Luteoviruses) are the most important and poorly understood.
Next Generation Sequencing (NGS) has enabled viral diversity at the whole genome level to be investigated. In this paper we focus on the diversity of TuYV and TuYV-like viruses. Analysis of samples initially thought to be TuYV from infected pulse crops, shows there is a high degree of genetic variation. A few different TuYV-like variants have been found, some of which are recombinants containing a fragment of TuYV and appear to represent distinct species.
For one new recombinant virus identified we propose the name, Chickpea red leaf recombinant virus (CRLRV). This virus has been found throughout northern New South Wales in chickpea, lentils, field pea, faba bean, and marshmallow weed (Malva parviflora). Analysis of CRLRV genome showed a recombination event in the intergenic non-coding region between open reading frame (ORF) 2 and ORF-3. The 3’ end of CRLRV, which includes ORF-3, -4 and -5, share around 92% nucleotide identity to TuYV (Genebank: NC_003743). The 5’ end, ORF-0, -1 and -2, is from a currently unidentified virus and shared approximately 66% nt identity to Chickpea chlorotic stunt virus (CpCSV).
Viral diversity and recombination events reiterate the need for good diagnostic techniques to ensure effective resistance breeding and disease management.