Molecular characterization of a distinct bipartite begomovirus species infecting tomato in India.
A distinct bipartite begomovirus was found associated with tomato plants showing yellowing, curling, and crumpling of the leaves, in a sub-temperate region in India. The complete DNA-A and DNA-B components were amplified through rolling circle amplification (RCA) using Phi-29 DNA polymerase and characterized. The DNA-A of the isolate was comprised of 2,756 nucleotides, encoding six open reading frames (ORFs) and DNA-B that of 2,725 nucleotides, encoding two ORFs. Genome organization of the isolate was typical of an old world bipartite begomovirus. Comparisons showed that DNA-A and its intergenic region (IR) have the highest sequence identity (86% and 84%, respectively) with the Tomato leaf curl New Delhi virus (ToLCNDV; DQ116885) and some other begomoviruses (>84%) reported from cucurbits and tomato. This data suggested that the isolate is a distinct begomovirus species for which a name Tomato leaf curl Palampur virus (ToLCPMV) is proposed. DNA-B showed the maximum sequence identity (73%) with Tomato leaf curl New Delhi virus-India-[Pakistan:Dargai:T5/6:2001] (AY150305). The common region (CR) of DNA-A and DNA-B showed 94% sequence similarity with each other. In the present study, phylogenetic relationship of this new species was also established with different begomoviruses reported from tomato and other begomoviruses showing highest homologies with complete DNA-A and DNA-B sequences. ToLCPMV is being reported from a sub-temperate region in India which was previously unaffected by begomoviruses and its whitefly vector.
Kumar
Yogesh
Y
Plant Virus Lab, Institute of Himalayan Bioresource Technology (CSIR), Palampur, Himachal Pradesh, 176 061, India.
Hallan
Vipin
V
Zaidi
Aijaz A
AA
D053839:Begomovirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D016679:Genome, Viral; D007194:India; D018551:Solanum lycopersicum / Q000821:virology*; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology*; D017385:Sequence Homology
J Virol Methods. 2006 Jul;135(1):9-16
16513183
Virology. 1999 Dec 20;265(2):218-25
10600594
Virology. 2006 Jan 5;344(1):198-210
16364750
Virology. 2001 Jul 5;285(2):234-43
11437658
Arch Virol. 2008;153(4):783-821
18256781
Virology. 2004 Jun 20;324(1):37-47
15183051
Arch Virol. 2001 Aug;146(8):1599-606
11676420
J Virol Methods. 2008 Feb;147(2):351-4
18022703
J Gen Virol. 1995 Feb;76 ( Pt 2):249-63
7844548
J Mol Biol. 1990 Oct 5;215(3):403-10
2231712
J Gen Virol. 2000 Jan;81(Pt 1):287-97
10640569
Nucleic Acids Res. 2003 Jul 1;31(13):3688-91
12824395
J Virol. 2004 Dec;78(24):13966-74
15564504
Trends Plant Sci. 2003 Mar;8(3):128-34
12663223
Arch Virol. 2007;152(5):941-54
17226067
J Virol Methods. 2004 Mar 15;116(2):209-11
14738990
J Virol Methods. 2008 Feb;147(2):355-9
18031835
Arch Virol. 2005 Oct;150(10):2151-79
16132185