Molecular characterization of a distinct begomovirus species from Vernonia cinerea and its associated DNA-beta using the bacteriophage Phi 29 DNA polymerase.
Vernonia cinerea plants with yellow vein symptoms were collected around crop fields in Madurai. A portion (550 bp) of the AV1 gene amplified using degenerate primers from the total DNA purified from diseased leaf sample was cloned and sequenced. Specific primers derived from the above sequence were used to amplify 2,745 nucleotides with the typical genome organization of begomoviral DNA A (EMBL Accession No. AM182232). Sequence comparison with other begomoviruses revealed the greatest identity (82.4%) with Emilia yellow vein virus (EmYVV-[Fz1]) from China and less than 80% with all other known begomoviruses. The International Committee on Taxonomy of Viruses (ICTV) has therefore recognized Vernonia yellow vein virus (VeYVV) as a distinct begomovirus species. Conventional PCR could not amplify the DNA B or DNA beta from the diseased tissue. However, the beta DNA (1364 bp) associated with the disease was obtained (Accession No. FN435836) by the rolling circle amplification-restriction fragment length polymorphism method (RCA-RFLP) using Phi 29 DNA polymerase. Sequence analysis shows that DNA beta of VeYVV has the highest identity (56.8%) with DNA beta of Sigesbeckia yellow vein Guangxi betasatellite (SibYVGxB-[CN: Gx111:05]) and 56-53% with DNA beta associated with other begomoviruses. This is the first report of the molecular characterization of VeYVV from V. cinerea in India. The complete molecular characterization, phylogenetic analysis, and putative recombination events in VeYVV are reported.
Packialakshmi
R M
RM
Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, 625 021, India.
Srivastava
N
N
Girish
K R
KR
Usha
R
R
D017103:Bacillus Phages / Q000201:enzymology / Q000235:genetics*; D001483:Base Sequence; D053839:Begomovirus / Q000235:genetics*; D004259:DNA-Directed DNA Polymerase / Q000235:genetics* / Q000378:metabolism; D016679:Genome, Viral; D008969:Molecular Sequence Data; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology*; D011995:Recombination, Genetic; D016415:Sequence Alignment; D035741:Vernonia / Q000821:virology*
D004259:DNA-Directed DNA Polymerase
Arch Virol. 2007;152(6):1147-57
17294343
Bioinformatics. 2000 Jun;16(6):562-3
10980155
J Mol Evol. 1994 Mar;38(3):300-4
8006997
Crit Rev Biochem Mol Biol. 2000;35(2):105-40
10821479
J Biol Chem. 1989 May 25;264(15):8935-40
2498321
Arch Virol. 2008;153(4):783-821
18256781
Virology. 2003 Jan 20;305(2):310-7
12573576
Genome Res. 2001 Jun;11(6):1095-9
11381035
Proc Natl Acad Sci U S A. 1983 Feb;80(3):726-30
6572363
J Mol Evol. 1992 Feb;34(2):126-9
1556748
Proc Natl Acad Sci U S A. 2001 Nov 20;98(24):13757-62
11717435
Arch Virol. 2008;153(4):763-81
18247103
J Gen Virol. 1997 Aug;78 ( Pt 8):2101-11
9267014
Phytopathology. 2003 Jul;93(7):774-83
18943157
Virus Res. 2007 Jan;123(1):9-18
16949698
Virology. 1999 Dec 20;265(2):218-25
10600594
Trends Genet. 2000 Jun;16(6):276-7
10827456
Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387-95
6546423
Mol Biotechnol. 2002 Mar;20(3):315-8
11936260
J Gen Virol. 2008 Sep;89(Pt 9):2063-2074
18753214
J Virol. 2006 Dec;80(23):11827-32
16971423
Mol Biol Evol. 1987 Jul;4(4):406-25
3447015
J Virol. 2003 Mar;77(5):2972-80
12584322
Proc Natl Acad Sci U S A. 1995 Apr 25;92(9):3879-83
7732000
Comput Appl Biosci. 1988 Mar;4(1):11-7
3382986
J Gen Virol. 2007 Nov;88(Pt 11):3154-3165
17947543
Gene. 1993 Dec 22;136(1-2):369-70
8294034
Cell Mol Life Sci. 1999 Oct 15;56(3-4):313-29
11212359