Identification and characterization of two novel genomic RNA segments RNA5 and RNA6 in rose rosette virus infecting roses

Abstract

Rose rosette virus (RRV), a negative-strand RNA virus belonging to the genus Emaravirus, has recently been characterized to be the causal agent of rose rosette disease. Roses showing typical symptoms of RRV collected from a rose nursery in Florida were subjected to reverse transcription-PCR (RT-PCR) assay using primers corresponding to the conserved inverted 13 nucleotide long stretches found at the termini of the RRV genomic RNA segments. RT-PCR analysis yielded two novel genomic RNA segments, RNA5 and RNA6, in addition to the previously identifi ed four RNA segments. Th e RNA5 is 1650 bp long and encodes for a polypeptide of 465 amino acids (54.3 K), while RNA6 is 1400 bp long and encodes for a polypeptide of 233 amino acids (27.05 K). RACE analysis showed that, both the RNA segments posses at their 5' and 3' termini, stretches of conserved inverted complementary13 nucleotides long sequence with two nucleotide mismatches as previously identifi ed in other genomic RNA segments. Northern blot analysis as well as RT-PCR using specifi c primers showed the presence of the novel genomic RNA segments in infected plants, but absent in the non-infected plants. Th e GenBank Acc. Nos. for the sequences reported in this paper are KT007556 and KT007557.

Variability of Emaravirus Species Associated with Sterility Mosaic Disease of Pigeonpea in India Provides Evidence of Segment Reassortment

“…In recent years, there have been increased reports of previously unidentified emaravirus species and their genomic RNA segments. Additional genomic segments, including RNA5 and RNA6 of FMV and RRV [ 12 , 38 , 39 ] and RNA4, RNA5 and RNA6 of RLBV, have recently been reported [ 40 , 41 ]. Recently eight genomic RNA segments were reported for WMoV [ 16 ].…”

Characterization of Rose rosette virus and development of reverse genetic system for studying virus accumulation and movement in whole plants

“…4E). Similar primer sets were reported in Babu et al (2016) to produce intermediate length and full length amplicons (3). In these experiments (Fig.…”

“…The first report of RRV genome sequence identified four segments and then a subsequent report identified three additional segments (2, 3). From these reports it is not clear whether the first four segments are the essential elements for infection, or if all seven segments are essential.…”

“…Initially, RRV was reported to have 4 genomes segments. RNAs 5, 6 and 7 were identified and sequences were reported in NCBI between 2014 and 2016 (3). Here we report the first-generation binary RRV infectious clones that produce all seven RNA segments.…”

The Plant Negative-Sense RNA Virosphere: Virus Discovery Through New Eyes

“…Finally, partial fragments of RNAs1, 2 and 4 of a putative novel emaravirus infecting alfalfa in Australia, named alfalfa ringspot-associated virus were recently identified using HTS ( Samarfard et al, 2020 ). PCR amplification of the conserved termini of the genome segments ( Babu et al, 2016 ) and HTS could be used to characterize the complete genome sequence of this tentative novel emaravirus.…”