Inference on Coat Protein Evolution of Lily Symptomless Carlavirus in India and Abroad Based on Motifs Study and Phylogenetic Analysis

Abstract

Lily symptomless carlavirus (LSV), the most common lily infecting virus around the world, contains 6 open reading frames (ORFs) in its genome, of which ORF5 representing coat protein (CP) is the most variable region and is used here to deduce phylogeny of the virus. CP gene of one of the LSV isolates present in the region, LSV isolate-Oh (Accession no. AJ748277) was taken as test sequence.Multiple sequence alignment of test sequence with ClustalW showed nucleotide and amino acid homology of up to 17-98% and 1-98%, respectively with other 78 carlaviral sequences from India and abroad. One conserved nucleotide motif of carlaviruses, AATAAA (Polyadenylation signal motif) was searched for, in the multiple sequence alignments but it was not found in any of the LSV isolates under study. Further, phylogenetic analysis of nucleotide sequences by DNADIST method of Neighbor-joining algorithm placed test LSV isolate most closely to its native LSV isolates from India and, LSV isolates Yunnan and Lanzou, from China. It could be interpreted that in Lily symptomless carlavirus at nucleotide level, evolution is taking place at a faster pace. Also, this virus shared its most recent common ancestry (MRCA), both with its native LSV isolates from India and as well as with LSV isolates from China, probably, indicating its origin from either of the countries. This study provides important clues about spread of the virus and to the best of our knowledge it is the first detailed study of LSV coat protein gene performed at nucleotide level.