LSV coat protein genes cloning and protein analyses

A pair of primers are designed and synthesized based on the oligosaccharides nucleotide sequences of coat protein (CP) genes of lily symptomless virus (LSV) reported, then, a fragment of 876 bp of LSV CP gene sequence is amplified by reverse transcription polymerase chain reaction (RT-PCR) from the total RNA infected lily leaves. The function and the secondary structure of LSV CP are predicted by the bioinformatics software system after analyzing the sequence. The results show that the gene is 876 bp in length coding 291 amino acids. This isolation has a homology of 93.4%-99.0% at nucleotide and 84.8%-99.5% at amino acid levels respectively compared with those published sequences of LSV according to GeneBank. The functional study prediction shows that the grand average of hydropathicity is -0.432. The protein has one coiled-coil domain, several phosphorylation sites and a conserved structure domain of Carlaviruses CP. The secondary structure is mainly composed of α-helix and random coil-based structures.