Biological and molecular characterization of two closely related carlaviruses affecting brassica plants

Abstract

Carlaviruses are plant-infecting viruses with flexuous filamentous particles of approximately 650 nm in length and a positive single-stranded hexacistronic RNA molecule as the genome. In this study, we analysed 14 samples of brassicas plants, reportedly affected by carlaviruses, that were collected in distant and edaphoclimatic distinct regions in Brazil. The genomes of four viral isolates detected in leaf kale (Brassica oleracea var. acephala) plants displayed the typical genomic organization of carlaviruses, subdivided into two contrasting identity profiles. Isolates T25, T107, and T110 showed a higher sequence identity among them (c.93%) than with T90 (c.67%), which had the highest nucleotide sequence identity (85.2%) with the only documented genomic fragment, approximately 1 kb of the RNA 3′-end, of cole latent virus (CoLV). Identity values among the other three isolates and CoLV were consistently lower than 78.6%. Nucleotide and amino acid sequence identity values of the replicase cistron of the isolates T25 and T90 are below the threshold for species demarcation in the genus Carlavirus. Upon mechanical transmission, these two isolates induced different symptoms in brassicas and solanaceous plants. Overall, data indicated that these viruses belong to two related but distinct species of carlaviruses. While T90 was recognized as an isolate of CoLV, the remaining isolates were considered members of a new tentative carlavirus named Cole mild mosaic virus (CoMMV). Current work provides convincing support for the taxonomic status of the species Cole latent virus, enlarges the known diversity of carlaviruses, and makes available new molecular tools to improve surveys of brassica-infecting viruses.