Complete nucleotide sequences of three dsRNA segments from Raphanus sativus-root cv. Yipinghong with leaf yellow edge symptoms

Abstract

The two minor dsRNA bands, previously detected in symptomatic leaves of Raphanus sativus-root cv. Yidianhong [corrected] were subjected to further analysis. cDNA cloning and sequencing revealed that the smaller of the two dsRNA bands is actually a doublet consisting of two co-migrating dsRNA segments and the resulting three segments were designated as RasR 3, RasR 4, and RasR 5. RasR 3 was 1717 bp in length and potentially encoded a protein of about 55.3 kDa, containing all of the six conserved motifs shared by the RNA dependent RNA polymerases of members of the family Partitiviridae. RasR 4 and RasR 5, which co-migrated in the 5% polyacrylamide gel, were 1521 and 1485 bp in length and each encoded a putative protein of unknown function. Their molecular masses, as calculated from the deduced amino acid, were 38.2 and 38.8 kDa, respectively. The 5' UTRs of all three segments shared regions of high sequence similarities, but were distinct from those of the RasR 1 and RasR 2. Taken together, these results along with those described in the previous report, suggest that more than one partitivirus was co-infecting radish leaves.

Nucleotide sequence of the tripartite Fragaria chiloensis cryptic virus and presence of the virus in the Americas

“…RNAs 2 and 3 are also monocistronic with open reading frames (ORF) spanning between nt 191-1237 of RNA 2 and nt 172-1212 of RNA 3. The putative 39 kDa proteins are most closely related to each other (23% aa identity, 43% aa similarity) and the putative proteins encoded by RNAs 4 and 5 (RasR 4 and RasR 5, respectively) from Raphanus sativus-root [21], than any other proteins found in the databases. Structural analysis of the putative proteins (data not shown) [12] show near identical folding of the proteins indicating that they are probably involved in the same function.…”

“…RNA 1 encodes a single protein that starts at nt 183 and terminates at nt 1622. Database searches indicated that the 56 kDa protein has core RNA-dependent RNA polymerases (RdRp) motifs between residues 164 and 363 [20] and is most closely related to the RdRps of RNA 3 from Raphanus sativus-root (RasR 3) [21] with 60% amino acid (aa) identity (76% aa similarity) and Beet cryptic virus-3 (BCV-3) [22] with 34% aa identity (56% aa similarity) [23] (Fig. 3).…”

The genome of Beet cryptic virus 1 shows high homology to certain cryptoviruses present in phylogenetically distant hosts

“…No other gene products have yet been described. Complete genome sequences are available for many fungal partitiviruses, currently classified in the genus Partitivirus, and during the last few years several sequences have been reported for plant viruses in the genus Alphacryptovirus, but none for betacryptoviruses [5][6][7][8][9][10][11][12][13][14]. Sequence comparisons fully support the relatedness of fungal and plant partitiviruses, moreover, they clearly show that similarity between certain plant and fungal viruses may be higher than similarity among the plant viruses [11].…”

“…The 3 0 -UTRs of the plus strand of dsRNA1 and dsRNA2 differ in length even more (64 and 191 nucleotides, respectively) and, like other members of Partitiviridae, they are also rich in adenosine and uracil bases [8,11,40]. Both dsRNAs contain a 22-and 27-nt long poly(A) tail.…”

Use of standard and setup of non conventional techniques for the elimination of viruses associated with Fig Mosaic Disease (FMD) in fig germplasm (Ficus carica L.)

“…However, some cryptic viruses have been reported to possess genomes consisting of three monocistronic dsRNA segments (Chen et al, 2006;Salem et al, 2008).…”