Complete nucleotide sequence and genetic organization of Sunflower mild mosaic virus (SuMMoV)

 Two potyviruses that infect sunflower (Helianthus annuus L.) crops have been reported in Argentina. Sunflower chlorotic mottle virus (SuCMoV) is the most widely distributed one, with two strains: common and ring spot, which have been completely characterized. Sunflower mild mosaic virus (SuMMoV) that produces a chlorotic mild mosaic on sunflower commercial crops was detected in the rural area of Paraná (Entre Ríos Province). This virus has been biologically and serologically characterized but not fully characterized at the molecular level. The aim of this work was to determine the complete sequence of SuMMoV and study its genomic organization.  A total RNA extraction was made from a preparation enriched with this virus. The quality of preparation was confirmed through electron microscopy and RT-PCR with specific primers for capsid protein gene. Total RNA obtained was pyrosequenced and the sequences obtained were analyzed.  Electron microscopy from rapid preparations of samples enriched with the virus showed high concentration of potyvirus-like particles. RT-PCR showed an aplicon of expected size. The pyrosequencing resulted in a large contig of 9686 nucleotides (nt) with a single open reading frame (ORF) of 3077 amino acids (aa). The ORF showed the highest levels of identity with Tobacco etch virus (TEV-L38714), 55.0% for nt and 54.8% for aa. The deduced genome organization is typical for a member of the Potyviridae family, and 10 common proteins mentioned for Potyvirus were identified: P1 (300 aa), HC-Pro (460 aa), P3 (349 aa), 6K1 (52 aa), CI (634 aa), 6K2 (53 aa), NIa-VPg (188 aa), NIa-Pro (241 aa), Nib (513 aa) and CP (287 aa). Nine putative protease cleavage sites were predicted computationally and by analogy with genome arrangements of other potyviruses.  These results confirm that the SuMMoV is a member of Potyvirus genus, Potyviridae family that infects sunflower in Argentina and this is the first report of a full sequence of its genome.  This study will contribute to understand its biology, diversity, evolution and begin molecular studies to obtain tolerance/resistance to disease.