Phylogenetic Analysis of Citrus tristeza virus Isolates of Wild Type Citrus in China
YI Long, ZHOU Chang-yong
1、Citrus Research Institute, Chinese Academy of Agricultural Sciences, Chongqing 400712, P.R.China
2、National Navel Orange Engineering Technology Research Center, Ganzhou 341000, P.R.China
摘要 The genetic variation and phylogenetic relationships of Citrus tristeza virus (CTV) isolates collected from Chinese wild type citrus were analyzed by comparing the sequences of nine genomic regions (p23, p20, p13, p18, p25, p27, POL, HEL and k17) with the CTV isolates of cultivated citrus from different countries. The results showed that the divergence pattern of genomic RNA of the CTV isolates from wild type citrus was similar to that of other isolates from cultivated citrus, the 3´ proximal region was relatively conserved, and the 5´ proximal region had greater variability. The nine genomic regions of CTV isolates analyzed were found to have been under purifying selection in the evolution process. Phylogenetic analysis showed that the eleven Chinese wild CTV isolates were located at different clades and did not reflect their geographical origins, suggesting genetic diversity among the Chinese wild CTV populations. These results will aid in the understanding of molecular evolution of the Chinese CTV populations.
Abstract The genetic variation and phylogenetic relationships of Citrus tristeza virus (CTV) isolates collected from Chinese wild type citrus were analyzed by comparing the sequences of nine genomic regions (p23, p20, p13, p18, p25, p27, POL, HEL and k17) with the CTV isolates of cultivated citrus from different countries. The results showed that the divergence pattern of genomic RNA of the CTV isolates from wild type citrus was similar to that of other isolates from cultivated citrus, the 3´ proximal region was relatively conserved, and the 5´ proximal region had greater variability. The nine genomic regions of CTV isolates analyzed were found to have been under purifying selection in the evolution process. Phylogenetic analysis showed that the eleven Chinese wild CTV isolates were located at different clades and did not reflect their geographical origins, suggesting genetic diversity among the Chinese wild CTV populations. These results will aid in the understanding of molecular evolution of the Chinese CTV populations.
This work was supported by the National Natural Science Foundation of China (30900977), the Program for Changjiang Scholars and Innovative Research Team in Universities, China (PCSIRT, IRT0976), the Key Project 210111 of Ministry of Education of China, and the Young Scientist Cultivation Program of Jiangxi, China (2010DQ02300).
YI Long, ZHOU Chang-yong.
2014.
Phylogenetic Analysis of Citrus tristeza virus Isolates of Wild Type Citrus in China. Journal of Integrative Agriculture, 13(12): 2669-2677.
Albiach-Martí M R, Guerri J, de Hermoso Mendoza A, LaigretF, Ballester-Olmos J F, Moreno P. 2000. Aphid transmissionalters the genomic and defective RNA populations ofCitrus tristeza virus isolates. Phytopathology, 90, 134-138
Albiach-Martí M R, Mawassi M, Gowda S, Satyanarayana T,Hilf M E, Shanker S, Almira E C, Vives M C, López C,Guerri J, Flores R, Moreno P, Garnsey S M, Dawson W O.2000. Sequences of Citrus tristeza virus separated in timeand space are essentially identical. Journal of Virology,74, 6856-6865
Ayllón M A, López C, Navas-Castillo J, Garnsey S M, Guerri J,Flores R, Moreno P. 2001. Polymorphism of the 5´ terminalregion of Citrus tristeza virus (CTV) RNA: Incidence ofthree sequence types in isolates of different origin andpathogenicity. Archives of Virology, 146, 27-40
Bar-Joseph M, Marcus R, Lee R F. 1989. The continuouschallenge of Citrus tristeza virus control. Annual Reviewof Phytopathology, 27, 291-316
Bernardi G. 1995. The human genome: Organization andevolutionary history. Annual Review of Genetics, 29,445-476
Castresana J. 2002. Genes on human chromosome 19 showextreme divergence from the mouse orthologs and a highGC content. Nucleic Acids Research, 30, 1751-1756
Fagoaga C, López C, Moreno P, Navarro L, Flores R, PeñaL. 2005. Viral-like symptoms induced by the ectopic expression of the p23 gene of Citrus tristeza virus arecitrus specific and do not correlate with the pathogenicityof the virus strain. Molecular Plant-Microbe Interactions,18, 435-445
Febres V J, Ashoulin L, Mawasi M, Frank A, Bar-JosephM, Manjunath K L, Lee R F, Niblett C L. 1996. Thep27 protein is present at one end of Citrus tristeza virusparticles. Phytopathology, 86, 1331-1335
Fullerton S M, Carvalho A B, Clark A G. 2001. Local rates ofrecombination are positively correlated with GC contentin the human genome. Molecular Biology and Evolution,18, 1139-1142
Gowda S, Satyanarayana T, Davis C L, Navas-Castillo J,Albiach-Martí M R, Mawassi M, Valkov N, Bar-JosephM, Moreno P, Dawson W O. 2000. The p20 gene productof Citrus tristeza virus accumulates in the amorphousinclusion bodies. Virology, 274, 246-254
Hall T A. 1999. BioEdit: a user-friendly biological sequencealignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95-98
Hardison R C, Roskin K M, Yang S, Diekhans M, Kent WJ, Weber R, Elnitski L, Li J, O’Connor M, Kolbe D,Schwartz S, Furey T S, Whelan S, Goldman N, Smit A,Miller W, Chiaromonte F, Haussler D. 2003. Co-variationin frequencies of substitution, deletion, transpositionand recombination during eutherian evolution. GenomeResarch, 13, 13-26
Hilf M E, Karasev A V, Albiach-Marti M R, Dawson W O,Garnsey S M. 1999. Two paths of sequence divergencein the Citrus tristeza virus complex. Phytopathology, 89,336-342
Hilf M E, Karasev A V, Pappu H R, Gumpf D J, Niblett CL, Garnsey S M. 1995. Characterization of Citrus tristezavirus subgenomic RNAs in infected tissue. Virology, 208,576-582
Hilf M E, Mavrodieva V A, Garnsey S M. 2005. Geneticmarker analysis of a global collection of isolates ofcitrus tristeza virus: Characterization and distributionof CTV genotypes and association with symptoms.Phytopathology, 95, 909-917
Karasev A V, Boyko V P, Gowda S, Nikolaeva O, Hilf M E,Koonin E V, Niblett C L, Cline K, Gumpf D J, Lee R F,Lewandowski D J, Dawson W O. 1995. Complete sequenceof the Citrus tristeza virus RNA genome. Virology, 208,511-520
Kumar S, Nei M, Dudley J, Tamura K. 2008. MEGA: Abiologist-centric software for evolutionary analysis ofDNA and protein sequences. Briefings in Bioinformatics,9, 299-306
López C, Ayllón M A, Navas-Castillo J, Guerri J, MorenoP, Flores R. 1998. Molecular variability of the 5´- and3´-terminal regions of Citrus tristeza virus RNA.Phytopathology, 88, 685-691
López C, Navas-Castillo J, Gowda S, Moreno P, Flores R.2000. The 23-kDa protein coded by the 3´-terminal gene ofCitrus tristeza virus is an RNA-binding protein. Virology,269, 462-470
Lu R, Folimonov A, Shintaku M, Li W X, Falk B W, DawsonW O, Ding S W. 2004. Three distinct suppressors ofRNA silencing encoded by a 20-kb viral RNA genome.Proceedings of the National Academy of Sciences of theUnited States of America, 101, 15742-15747
Martín S, Sambade A, Rubio L, Vives M C, Moya P, Guerri J,Elena S F, Moreno P. 2009. Contribution of recombinationand selection to molecular evolution of Citrus tristezavirus. Journal of General Virology, 90, 1527-1538
Mawassi M, Mietkiewska E, Gofman R, Yang G, Bar-JosephM. 1996. Unusual sequence relationships between twoisolates of Citrus tristeza virus. Journal of GeneralVirology, 77, 2359-2364
Melzer M J, Borth W B, Sether D M, Ferreira S, GonsalvesD, Hu J S. 2010. Genetic diversity and evidence forrecent modular recombination in Hawaiian Citrustristeza virus. Virus Genes, 40, 111-118
Roy A, Brlansky R H. 2010. Genome analysis of an orangestem pitting Citrus tristeza virus isolate reveals a novelrecombinant genotype. Virus Research, 151, 118-130
Rubio L, Ayllón M A, Kong P, Fernández A, Polek M,Guerri J, Moreno P, Falk B W. 2001. Genetic variation ofCitrus tristeza virus isolates from California and Spain:evidence for mixed infections and recombination. Journalof Virology, 75, 8054-8062
Ruiz-Ruiz S, Moreno P, Guerri J, Ambrós S. 2006. Thecomplete nucleotide sequence of a severe stem pittingisolate of Citrus tristeza virus from Spain: Comparisonwith isolates from different origins. Archives of Virology,151, 387-398
Ruiz-Ruiz S, Navarro B, Gisel A, Peña L, Navarro L, MorenoP, Serio F D, Flores R. 2011. Citrus tristeza virus infectioninduces the accumulation of viral small RNAs (21-24-nt)mapping preferentially at the 3´-terminal region of thegenomic RNA and affects the host small RNA profile Plant Molecular Biology, 75, 607-619
Satyanarayana T, Gowda S, Ayllón M A, Albiach-Martí M R,Rabindran S, Dawson W O. 2002. The p23 protein of Citrustristeza virus controls asymmetrical RNA accumulation.Journal of Virology, 76, 473-483
Satyanarayana T, Gowda S, Mawassi M, Albiach-Martí M R,Ayllón M A, Robertson C, Garnsey S M, Dawson W O.2000. Closterovirus encoded HSP70 homolog and p61 inaddition to both coat proteins function in efficient virionassembly. Virology, 278, 253-265
Sentandreu V, Castro J A, Ayllon M A, Rubio L, GuerriJ, Gonzalez-Candelas F, Moreno P, Moya A. 2006.Evolutionary analysis of genetic variation observed inCitrus tristeza virus (CTV) after host passage. Archivesof Virology, 151, 875-894
Suastika C, Natsuake T, Hirotsugu T, Kano T, Ieki H, Okuda S. 2001. Nucleotide sequence of Citrus tristeza virus seedlingyellows isolate. Journal of General Plant Pahtology, 67,73-77
Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4:Molecular evolutionary genetics analysis (MEGA)software version 4.0. Molecular Biology and Evolution,24, 1596-1599
Tatineni S, Robertson C J, Garnsey S M, Bar-Joseph M, GowdaS, Dawson W O. 2008. Three genes of Citrus tristeza virusare dispensable for infection and movement throughoutsome varieties of citrus trees. Virology, 376, 297-307
Thompson J D, Higgins D G, Gibson T J. 1994. CLUSTAL W:Improving the sensitivity of progressive multiple sequencealignment through sequence weighting, position-specificgap penalties and weight matrix choice. Nucleic AcidsResearch, 22, 4673-4680
Vives M C, Rubio L, López C, Navas-Castillo J, Albiach-MartíM R, Dawson W O, Guerri J, Flores R, Moreno P. 1999.The complete genome sequence of the major componentof a mild Citrus tristeza virus isolate. Journal of GeneralVirology, 80, 811-816
Yang Z N, Mathews D M, Dodds J A, Mirkov T E. 1999.Molecular characterization of an isolate of Citrus tristezavirus that causes severe symptoms in sweet orange. VirusGenes, 19, 131-142
Yi L, Zhou C Y, Zhou Y, L i Z A. 2010. Genetic evolutionanalysis on wild isolates of Citrus tristeza virus originatedin China based on coat protein genes sequences.Agricultural Sciences in China, 11, 1623-1629
Yi L, Zhou C Y, Zhou Y, Wang Z G, Tang K Z. 2007.Molecular characterization of Citrus tristeza virus isolatesin Chinese wild type citrus. Scientia Agricultura Sinica,40, 932-939. (in Chinese)
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