Molecular variability analyses of Apple chlorotic leaf spot virus capsid protein

Journal of Biosciences

Volumn 35, Issue 4, 2010, Pages 605-615

  Rana, T ^a   Chandel, V ^a   Kumar, Y ^a   Ram, R ^a   Hallan, V ^a   Zaidi, A A ^a  

^a CSIR INSTITUTE OF HIMALAYAN BIORESOURCE TECHNOLOGY   (India)

Author keywords

ACLSV; coat protein; India; phylogenetic analysis; recombination; variability

Indexed keywords

CAPSID PROTEIN;

AMINO ACID; GENETIC ANALYSIS; LEAF; MOLECULAR ANALYSIS; PHYLOGENETICS; PROTEIN; RECOMBINATION;

ALMOND; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; AMINO TERMINAL SEQUENCE; APPLE; APRICOT; ARTICLE; CARBOXY TERMINAL SEQUENCE; CHERRY; CHLOROSIS; ENZYME LINKED IMMUNOSORBENT ASSAY; HOST RANGE; INDIA; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PEACH; PEAR; PHYLOGENY; PLUM; QUINCE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; TRICHOVIRUS; VIRUS ISOLATION; VIRUS RECOMBINATION;

AMINO ACID SEQUENCE; CAPSID PROTEINS; FLEXIVIRIDAE; INDIA; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANT LEAVES; RECOMBINATION, GENETIC; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

INDIA;

APPLE CHLOROTIC LEAF SPOT VIRUS; APRICOT PSEUDO-CHLOROTIC LEAF SPOT VIRUS; CHERRY MOTTLE LEAF VIRUS; CYDONIA OBLONGA; MALUS X DOMESTICA; MIRIDAE; PEACH MOSAIC VIRUS; PRUNUS ARMENIACA; PRUNUS DOMESTICA; PRUNUS DULCIS; PRUNUS PERSICA; PYRUS;

EID: 78651287069     PISSN: 02505991     EISSN: 02505991     Source Type: Journal    
DOI: 10.1007/s12038-010-0069-4     Document Type: Article

References (36)

1. M. J. Adams J. F. Antoniw M. Bar-Joseph A. A. Brunt T. Candresse G. D. Foster G. P. Martelli R. G. Milne S. K. Zavriev C. M. Fauquet 2004 The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation Arch. Virol. 149 1045 1060 1:CAS:528:DC%2BD2cXjt1Sgtr4%3D 15098118
2. M. Al-Rawahnih C. Turturo A. Minafra P. Saldarelli A. Myrta V. Pallas V. Savino 2004 Molecular variability of Apple chlorotic leaf spot virus in different hosts and geographic regions J. Plant Pathol. 86 117 122
3. Burnt A A, Crabtree K, Dallwitz M J, Gibbs A J and Watson L (eds.) 1996 Viruses of plants-descriptions and lists from the VIDE database (UK: CAB International, Wallingford) pp 100
4. A. Callaway D. Giesman-Cookmeyer E. T. Gillock T. L. Sit S. A. Lommel 2001 The multifunctional capsid proteins of plant RNA viruses Ann. Rev. Phytopath. 39 419 460 1:CAS:528:DC%2BD3MXmvVygsb0%3D 10.1146/annurev.phyto.39.1. 419 (Pubitemid 32965192)
5. E. B. Carstens 2010 Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2009) Arch. Virol. 155 133 146 1:CAS:528:DC%2BC3cXkt1Cgug%3D%3D 10.1007/s00705-009-0547-x 19960211
6. T. Cembali R. J. Folwell P. Wandschneider K. C. Eastwell W. E. Howell 2003 Economic implications of a virus prevention program in deciduous tree fruits in the US Crop Protection 22 1149 1156 10.1016/S0261-2194(03)00156-X (Pubitemid 37365251)
7. M. F. Clark A. N. Adams 1977 Characteristics of the microplate method of enzyme-linked immunosorbent assay for the detection of plant viruses J. Gen. Virol. 34 475 483 1:STN:280:DyaE2s7mslWntQ%3D%3D 10.1099/0022-1317-34-3-475 323416
8. F. Corpet 1998 Multiple sequence alignment with hierarchical clustering Nuc. Acid. Res. 16 10881 10890 10.1093/nar/16.22.10881
9. J. C. Desvignes R. Boye 1989 Different diseases caused by chlorotic leaf spot virus on the fruit trees Acta Hort. 235 31 38
10. J. Dunez G. Marenaud R. P. Delbos M. Lansac 1972 Variability of symptoms induced by the Apple chlorotic leaf spot (CLSV). A type of CLSV probably responsible for bark split disease of prune trees Plant Dis. Rep. 56 293 295
11. S. German T. Candresse M. Lanneau J. C. Huet J. C. Pernollet J. Dunez 1990 Nucleotide sequence and genomic organization of Apple chlorotic leaf spot closterovirus Virology 179 104 112 1:CAS:528:DyaK3MXhsFOrtL0%3D 10.1016/0042-6822(90)90279-Z 2219716 (Pubitemid 20354321)
12. S. German R. P. Delbos T. Candresse M. Lanneau J. Dunez 1997 Complete nucleotide sequence of the genome of a severe cherry isolate of Apple chlorotic leaf spot trichovirus (ACLSV) Arch. Virol. 142 833 841 10.1007/s007050050122 (Pubitemid 27185686)
13. D. Higgins J. Thompson T. Gibson J. D. Thompson D. G. Higgins T. J. Gibson 1994 CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalities and weight matrix choice Nucleic. Acid. Res. 22 4673 4680 10.1093/nar/22.22.4673 7984417
14. J. Jelkmann 1996 The nucleotide sequence of a strain of Apple chlorotic leaf spot virus (ACLSV) responsible for plum pseudopox and its relation to an apple and plum back split strain Phylopathol. 86 10i
15. D. Liberti A. Marais L. Svanella-Dumas M. J. Dulucq D. Alioto A. Ragozzino B. Rodoni T. Candresse 2005 Characterization of Apricot pseudo-chlorotic leaf spot virus, a novel Trichovirus isolated from stone fruit trees Phytopathology 95 420 426 1:CAS:528:DC%2BD2MXjtlals7Y%3D 10.1094/PHYTO-95-0420 18943045 (Pubitemid 40398904)
16. G. Llacer M. Cambra A. Lavina J. Aramburu 1985 Suitable conditions for detecting apple chlorotic leaf spot virus in apricot trees by enzyme-linked immunosorbent assay (ELISA) Agronomie 5 809 812 10.1051/agro:19850906
17. R. Lu A. Folimonov M. Shintaku W. X. Li B. W. Falk W. O. Dawson S. W. Ding 2004 Three distinct suppressors of RNA silencing encoded by a 20-kb viral RNA genome Proc. Natl. Acad. Sci. USA 101 15742 15747 1:CAS:528: DC%2BD2cXhtVWisLnO 10.1073/pnas.0404940101 15505219 (Pubitemid 39473558)
18. D. B. Marini P. G. Gibson S. W. Scott 2008 The complete nucleotide sequence of an isolate of Apple chlorotic leaf spot virus from peach (Prunus persica (L.) Batch) Arch. Virol. 153 1003 1005 1:CAS:528:DC%2BD1cXksl2qs7s%3D 10.1007/s00705-008-0076-z 18392552
19. D. P. Martin C. Williamson D. Posada 2005 RDP2: recombination detection and analysis from sequence alignments Bioinformatics 21 260 262 1:CAS:528:DC%2BD2MXkt1Whug%3D%3D 10.1093/bioinformatics/bth490 15377507 (Pubitemid 40202028)
20. L. Nemchinov A. Hadidi T. Verderevskaya 1995 Detection and partial characterization of a Plum Pox Virus isolate from infected sour cherry Acta Hort. 386 226 236 1:CAS:528:DyaK2sXitFCltLw%3D
21. Németh M 1986 Viruses, mycoplasma and ricketsia diseases of fruit trees (Boston: Kluwer Academic Publishers Group) pp 840
22. J. Polák J. Svoboda 2006 The reliability of detection and the distribution of Apple chlorotic leafspot virus in pears in the Czech Republic Hort. Sci. 33 7 10
23. T. Rana V. Chandel V. Hallan A. A. Zaidi 2007 Himalayan wild cherry (Prunus cerasoides D. Don) as a new host of Apple chlorotic leaf spot virus For. Pathol. 38 73 77
24. T. Rana V. Chandel V. Hallan A. A. Zaidi 2008 Characterization of Apple chlorotic leaf spot virus infecting almonds in India Aust. Plant Path. 3 65 67
25. T. Rana V. Chandel V. Hallan A. A. Zaidi 2008 Cydonia oblonga as reservoir of Apple chlorotic leaf spot virus in India Plant Pathol. 156 382 384
26. T. Rana V. Chandel V. Hallan A. A. Zaidi 2008 Molecular evidence for Apple Chlorotic Leaf Spot Virus in wild and cultivated apricot in Himachal Pradesh, India J. Plant Pathol. 89 72
27. Sambrook J, Fritsch E F and Maniatis T 1989 Molecular cloning - a laboratory manual, 2nd edition (Cold Spring Harbor: Cold Spring Harbor Laboratory Press)
28. F. Sanger S. Nickelen A. R. Coulson 1977 DNA sequencing with chain termination inhibitors Proc. Natl. Acad. Sci. USA 74 5463 5467 1:CAS:528:DyaE1cXhtlaru7Y%3D 10.1073/pnas.74.12.5463 271968
29. K. Sato N. Yoshikawa T. Takahashi 1993 Complete nucleotide sequence of the genome of an apple isolate of Apple chlorotic leaf spot virus J. Gen. Virol. 74 1927 1931 1:CAS:528:DyaK2cXpslCktA%3D%3D 10.1099/0022-1317-74-9-1927 8376968
30. Sutic D D, Ford R E and Tosic M T 1999. Virus diseases of fruit trees. In: Handbook of plant virus diseases (Boca Raton: CRC Press) pp 345-347
31. K. Tamura J. Dudley M. Nei S. Kumar 2007 MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0 Mol. Biol. Evol. 24 1596 1599 1:CAS:528:DC%2BD2sXpsVGrsL8%3D
32. C. L. Thomas V. Leh C. Lederer A. J. Maule 2003 Turnip crinkle virus coat protein mediates suppression of RNA silencing in Nicotiana benthamiana Virology 306 33 41 1:CAS:528:DC%2BD3sXhs1Kntrc%3D 10.1016/S0042-6822(02)00018-1 12620795 (Pubitemid 36293393)
33. C. Ulubas F. Ertunc 2005 Apple Chlorotic Leaf Spot Virus (ACLSV) status in Turkey and sensitive detection using advanced techniques Turk. J. Agric. For. 29 251 257
34. Y. Q. Wu D. M. Zhang S.Y. Chen X. F. Wang W. H. Wang 1998 Comparison of three ELISA methods for the detection of Apple chlorotic leaf spot virus and Apple stem grooving virus Acta Hort. 472 55 60
35. H. Yaegashi M. Isogai H. Tajima T. Sano N. Yoshikawa 2007 Combinations of two amino acids (Ala40 and Phe75 or Ser40 and Tyr75) in the coat protein of Apple Chlorotic Leaf Spot Virus are crucial for infectivity J. Gen. Virol. 88 2611 2618 1:CAS:528:DC%2BD2sXhtVWnu7vL 10.1099/vir.0.82984-0 17698674 (Pubitemid 47323910)
36. N. Yoshikawa T. Takahashi 1988 Properties of RNAs and proteins of Apple stem grooving and Apple chlorotic leaf spot viruses J. Gen. Virol. 69 241 245 1:CAS:528:DyaL1cXht1yiu78%3D 10.1099/0022-1317-69-1-241