| Research Article |
Open Access |
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| Inference on Coat Protein Evolution of Lily Symptomless
Carlavirus in India and Abroad Based on Motifs Study and
Phylogenetic Analysis |
| Suhasini Huddone1†*, Satya Vrat Bhardwaj1, Rameshwar Singh Rattan2#, Kamlesh Kanwar1 , Gaurav Zinta1### and Anil Handa3 |
1Department of Biotechnology, Dr Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan (Himachal Pradesh) 173230, India
2Department of Entomology, Dr Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan (Himachal Pradesh) 173230, India
3Department of Plant Pathology, Dr Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan (Himachal Pradesh) 173230, India
†Current address: Department of Molecular Biology, Central Potato Research Institute, Shimla (Himachal Pradesh) 171001, India
#Current address: Institute of Himalayan Bioresource Technology, HATS, Palampur, (Himachal Pradesh) 176061, India
###Current Address: Department of Biology, University of Antwerp, Universiteitsplein 1, B 2610 Wilrijk, Belgium |
| *Corresponding author: |
Dr. Suhasini Huddone,
Department of Biotechnology,
Dr Y. S. Parmar University of Horticulture and Forestry,
Nauni, Solan (Himachal
Pradesh) 173230, India
E-mail: suhasinihuddone2010@gmail.com |
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| Received June 11, 2010; Accepted June 29, 2010; Published June 29, 2010 |
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| Citation: Suhasini H, Bhardwaj SV, Rattan RS, Kanwar K, Zinta G, et al. (2010)
Inference on Coat Protein Evolution of Lily Symptomless Carlavirus in India and
Abroad Based on Motifs Study and Phylogenetic Analysis. J Proteomics Bioinform
3: 204-211. doi:10.4172/jpb.1000141 |
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| Copyright: © 2010 Suhasini H, et al. This is an open-access article distributed
under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the
original author and source are credited.
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| 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.
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