Molecular characterization of the complete genome of a barley yellow dwarf virus-PAV isolate from Iran

BYDV-PAV is one of the major agents causing yellowing and dwarfing of cereals worldwide. Previous study has been report the wide distribution of BYDVs in Iran and the prevalence of BYDV-PAV in cereal fields of the country. Due to the importance of this virus, and to investigate the taxonomic position of the Iranian isolate, the full length sequence of an Iranian severe isolate of BYDV-PAV from Kerman province (KP771878) was determined. Total RNA was extracted usingRNX (-plus)TM Kit. Nucleic acid extracts were reverse transcribed and amplified using PAV specific primers. The amplified fragments were inserted into PTZ57R/T vector using Ins T/A clone PCR Product Kit (MBI Fermentas) and cloned in Escherichia coli (DH5α) and sequenced. Complete nucleotide sequence of this isolate comprises 5668 nucleotides. Sequence analysis at nucleotide level showed that the Kerman isolate has maximum homology of about 94% with two American isolates (AF235167 and EF043235) of BYDV-PAV and grouped in the same cluster, while it showed the least similarity with a Chinese isolate of BYDV-PAV (AY855920) with only 78% homology. In addition, nucleotide sequence comparison of each ORF showed that the ORF4 was the most conserved while the ORF6 was the most divergent regions.