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Recombination and phylogeographical analysis of Lily symptomless virus.

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Title Recombination and phylogeographical analysis of Lily
symptomless virus.
 
Creator Singh, A K
Mahinaghara, B K
Hallan, Vipin
Raja, Ram
Zaidi, A A
 
Subject Plant sciences
Plant viruses
 
Description 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.
 
Publisher Springer, Van Godewijckstraat 30, 3311 GZ Dordrecht, Netherlands
 
Date 2008
 
Type Article
PeerReviewed
 
Format application/pdf
 
Identifier http://ihbt.csircentral.net/264/1/virus_genes_paper.pdf
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
 
Relation http://ihbt.csircentral.net/264/