Identification and characterization of cardamom vein clearing virus, a novel aphid-transmitted nucleorhabdovirus

Abstract

The vein clearing (kokke kandu) disease suspected to be caused by an unknown virus is an important production constraint of cardamom in India. In the present study the causal virus was transmitted from infected to healthy cardamom plants through the aphid, Pentalonia caladii. Small RNA (sRNA) and RNA sequencing (RNA-seq) of the aphid-inoculated plant showed several nucleorhabdovirus-like contigs. The sRNA and RNA-seq results were verified through reverse transcription polymerase chain reaction (RT-PCR) using total RNA from infected plant and primers designed fromthe contigs. The cloning and sequencing of RT-PCR products resulted in a sequence of 13392 bases that showed similarities to nucleorhabdoviruses. Thesequenced region contained allsix open reading frames of the virusin the order 3'-N-P-P3-M-G-L-5'and showed nucleotide sequence identities ranging from 37-55% with nucleorhabdoviruses indicating its distinct nature for which we propose the name, cardamom vein clearing virus.A reliable RT-PCR and SYBR Green-based real-time RT-PCR assays were developed for the detection of the virus that willaid in the identification and propagation of virus-free cardamom plants.