Complete nucleotide sequences of two isolates of Sunflower chlorotic mottle virus (SuCMoV) obtained from different hosts

BEJERMAN, NICOLÁS; GIOLITTI, FABIÁN; DE BREUIL SOLEDAD; LENARDON, SERGIO

Congreso; 18th International Sunflower Conference; 2012

Sunflower chlorotic mottle virus (SuCMoV), which belongs to the genus Potyvirus, is the most prevalent sunflower virus present in Argentina. This virus has a widespread occurrence in Argentina, where it infects naturally sunflower (Helianthus annuus ), Helianthus petiolaris, Dipsacus fullonum and Ibicella lutea. Two biologically different strains of SuCMoV have been reported on sunflower: the common strain (C) and the chlorotic ringspot strain (CRS) and theirs genomes have been completely sequenced. The objective of this work was to sequence and analyze the complete genomes of two SuCMoV isolates, SuCMoV-dip, obtained from Dipsacus fullonum and SuCMoV-ibi obtained from Ibicella lutea to further characterize SuCMoV´s molecular variability and the genetic structure of its population. Total RNA was extracted from systematically infected plants and used as template to amplify the SuCMoV full-length genome using three specific primer pairs. The sequence of SuCMoV-dip and SuCMoV-ibi comprise 9962 nucleotides (nt), including both non-translated regions (5´-NCR with 152 nt and 3´-NCR with 257 nt, respectively). Both sequences include a large open reading frame (ORF) starting at position 135. The deduced amino acid (aa) sequences show a polyprotein with 3187 aa. The recently identified small ORF PIPO and the conserved G(1-2)A(6-7) motif associated with its putative frameshift translation were identified in the sequences of both isolates. The genomes of -dip and -ibi isolates are 1 aa longer than the SuCMoV-CRS genome, but 4 aa shorter than SuCMoV-C genome. Indels located in the N-terminal region of P1 determinate the difference in length within SuCMoV´s genome. A total of nine cleavage sites were identified in the polyproteins of both isolates. Those nine sites are completely conserved among the two isolates and the two strains of SuCMoV. The previously identified and highly conserved aa sequence motifs described in potyviruses, were identified in both SuCMoV isolates. Sequence comparison of the deduced aa sequences of isolates-dip and ?ibi with those of SuCMoV´s -C and -CRS strains, confirmed the identity of the two mentioned isolates as SuCMoV: they display more than 90% sequence identity with SuCMoV-C and ?CRS for the complete polyprotein. Most of the nt changes occurred at the 3rd codon position and most of them were silent. The most conserved region between -dip and -ibi isolates was the NIb coding region; In contrast, the P1 coding region, the N-terminal region of CP and PIPO were the most variable regions. Phylogenetic analysis based on the complete polyprotein aa sequences supported the results from sequence comparison. SuCMoV-dip and -ibi isolates formed a monophyletic cluster with SuCMoV-C and -CRS strains. We have determined the complete sequences of the genomes of two SuCMoV isolates from Dipsacus fullonum and Ibicella lutea. Our results demonstrate that there is a significant variation at the 5´-end of the SuCMoV´s genome. These results shed light into the SuCMoV´s variability and evolution.