Singh, A K and Mahinaghara, B K and Hallan, Vipin and Raja, Ram and Zaidi, A A (2008) Recombination and phylogeographical analysis of Lily symptomless virus. Virus Genes, 36 (2). pp. 421-427. ISSN 0920-8569

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The complete genomic nucleotide sequence of an Indian isolate of Lily symptomless virus (LSV) was determined by sequencing 11 overlapping cDNA fragments of different sizes. The genome consisted of 8,394 nucleotides, excluding the poly (A) tail and contained six open reading frames (ORFs) coding protein for ORF1 220 kDa [1,948 amino acid (aa)], ORF2 25 kDa (228 aa), ORF3 12 kDa (106 aa), ORF4 7 kDa (64 aa), ORF5 32 kDa (291 aa) and ORF6 16 kDa (140 aa) from 50 to 30 end. Sequence was analyzed with other previously characterized full genomes of LSV. Phylogenetic analysis on the basis of RNA-dependent RNA polymerase (RdRp), Triple gene block proteins (TGB’s), Coat protein (CP), and ORF6 (16 kDa protein) amino acid sequence revealed that Indian isolate is closely related to The Netherlands Isolate (AJ564638). The overall genome of the present LSV isolate shares 97–98% nucleotide sequence homology with the previously characterized isolates. The phylogenetic analysis, sequence alignment studies, and recombination detection program (RDP3) analysis provided evidence for the occurrence of recombination between the present isolate (AM422452) as major parent and The Netherlands Isolate (AJ564638) and Chinese isolate (AM263208) as minor parents in two different independent recombination events. Based on the recombination analysis, it is suggested that the 30 end of the present isolate is involved in recombination with Chinese isolate (AM263208) and gave rise to the Korean isolate. To the best of our knowledge, this is the first report of complete nucleotide sequence from India and also the first evidence of homologous recombination in LSV.

Item Type: Article
Uncontrolled Keywords: complete genome; recombination; LSV; phylogenetic analysis; RT-PCR; variability; Complete Nucleotide-Sequence; Mottle-Virus; Coat Protein; Latent-Virus; RNA Viruses; Evolution; Carlavirus; Alignment; Lilium
Subjects: Plant sciences
Plant viruses
Depositing User: Dr. Aparna Maitra Pati
Date Deposited: 27 Dec 2011 12:04
Last Modified: 13 Feb 2012 05:50

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