Genomic RNAs S and M of Tomato Necrotic Ringspot Virus, a Tospovirus Infecting Pepper and Tomato

Abstract

The recent wide spread of tospovirus disease in vegetable crops in Thailand with high incidence
rate in farmers’ fields was caused by Tomato necrotic ringspot virus, TNRV. The virus has also been
detected in seed production fields of some seed companies in Thailand. Knowledge of virus genetics will
lead efficient disease management, therefore in the present study, three isolates of TNRV were newly
isolated from pepper and tomato in Nakhon Pathom and Nong Khai provinces and their genomes were
characterized. Isolate T91 induced yellow spot local lesion on leaves of Vigna unguiculata, while the
other two isolates did not. All isolates caused systemic mosaic symptoms on leaves of Datura metel. Full
length RNA S of isolates CT1, C94 and T91 contained 3016, 3017 and 3015 nucleotides, respectively, and
full length RNA M contained 4716, 4736 and 4723 nucleotides, respectively. RNA S shared 95.1-99.2 %
nucleotide identities among three isolates while RNA M shared 94.0-97.2% identity. The length and nucleotide sequence of 5′ and 3′ untranslated regions and the intergenic regions varied. Genomic RNA
S and RNA M showed 95.1-98.8 % and 94.3-97.2 % identity to the previous reported TNRV isolate TT1 in
Thailand, but only 58.9 % identity to tospovirus group IV. In phylogenetic tree analysis all TNRV isolates
clustered together but separated from all previously reported tospovirus species.