The origin and evolution of geminivirus-related DNA sequences in Nicotiana

Heredity

Volumn 92, Issue 4, 2004, Pages 352-358

  Murad, L ^a   Bielawski, J P ^b   Matyasek, R ^a,c   Kovarik A ^c   Nichols, R A ^a   Leitch, A R ^a   Lichtenstein, C P ^a  

^a QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

^c INSTITUTE OF BIOPHYSICS   (Czech Republic)

Author keywords

Geminiviruses; Helitrons; Horizontal transmission; Nicotiana; Rolling circle replication

Indexed keywords

CYTOSINE; PLANT DNA; VIRUS DNA;

DNA; HORIZONTAL TRANSMISSION; HOST-PATHOGEN INTERACTION; VIRAL DISEASE;

ARTICLE; CHEMISTRY; DNA METHYLATION; DNA REPLICATION; GC RICH SEQUENCE; GEMINIVIRUS; GENETICS; HORIZONTAL GENE TRANSFER; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; TOBACCO;

BASE SEQUENCE; CYTOSINE; DNA METHYLATION; DNA REPLICATION; DNA, PLANT; DNA, VIRAL; EVOLUTION, MOLECULAR; GC RICH SEQUENCE; GEMINIVIRIDAE; GENE TRANSFER, HORIZONTAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; TOBACCO;

EMBRYOPHYTA; EUKARYOTA; GEMINIVIRIDAE; NICOTIANA; NICOTIANA KAWAKAMII; NICOTIANA TABACUM; NICOTIANA TOMENTOSA; NICOTIANA TOMENTOSIFORMIS; TRANSPOSONS;

EID: 1842508548     PISSN: 0018067X     EISSN: None     Source Type: Journal    
DOI: 10.1038/sj.hdy.6800431     Document Type: Article

References (32)

1. Ashby MK, Warry A, Bejarano ER, Khashoggi A, Burrell M, Lichtenstein CP (1997). Analysis of multiple copies of geminiviral DNA in the genome of four closely related Nicotiana species suggest a unique integration event. Plant Mol Biol 35: 313-321.
2. Baulcombe D (2001). RNA silencing - diced defence. Nature 409: 295-296.
3. Bejarano ER, Khashoggi A, Witty M, Lichtenstein C (1996). Integration of multiple repeats of geminiviral DNA into the nuclear genome of tobacco during evolution. Proc Natl Acad Sci USA 93: 759-764.
4. Bejarano ER, Lichtenstein CP (1994). Expression of TGMV antisense RNA in transgenic tobacco inhibits replication of BCTV but not ACMV geminiviruses. Plant Mol Biol 24: 241-248.
5. Bielawski JP, Dunn KA, Yang ZH (2000). Rates of nucleotide substitution and mammalian nuclear gene evolution: approximate and maximum-likelihood methods lead to different conclusions. Genetics 156: 1299-1308.
6. Bird AP (1986). CpG-rich islands and the function of DNA methylation. Nature 321: 209-213.
7. Brough CL, Gardiner WE, Inamdar NM, Zhang XY, Ehrlich M, Bisaro DM (1992). DNA methylation inhibits propagation of tomato golden mosaic-virus DNA in transfected protoplasts. Plant Mol Biol 18: 703-712.
8. Day AG, Bejarano ER, Buck KW, Burrell M, Lichtenstein CP (1991). Expression of an antisense viral gene in transgenic tobacco confers resistance to the DNA virus tomato golden mosaic-virus. Proc Natl Acad Sci USA 88: 6721-6725.
9. Dunn KA, Bielawski JP, Yang ZH (2001). Substitution rates in Drosophila nuclear genes: implications for translational selection. Genetics 157: 295-305.
10. Felsenstein J (1985). Confidence-limits on phylogenies - an approach using the bootstrap. Evolution 39: 783-791.
11. Feschotte C, Wessler SR (2001). Treasures in the attic: rolling circle transposons discovered in eukaryotic genomes. Proc Natl Acad Sci USA 98: 8923-8924.
12. Frederico LA, Kunkel TA, Shaw BR (1990). A sensitive genetic assay for the detection of cytosine deamination - determination of rate constants and the activation-energy. Biochemistry 29: 2532-2537.
13. Gibbs MJ, Weiller GF (1999). Evidence that a plant virus switched hosts to infect a vertebrate and then recombined with a vertebrate-infecting virus. Proc Natl Acad Sci USA 96: 8022-8027.
14. Goldman N, Yang ZH (1994). Codon-based model of nucleotide substitution for protein-coding DNA-sequences. Mol Biol Evol 11: 725-736.
15. Hanley-Bowdoin L, Settlage SB, Orozco BM, Nagar S, Robertson D (2000). Geminiviruses: models for plant DNA replication, transcription, and cell cycle regulation. Crit Rev Biochem Mol Biol 35: 105-140.
16. Hasegawa M, Kishino H, Yano TA (1985). Dating of the human ape splitting by a molecular clock of mitochondrial-DNA. J Mol Evol 22: 160-174.
17. Higgins DG, Sharp PM (1998). CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73: 237-244.
18. Kapitonov VV, Jurka J (2001). Rolling-circle transposons in eukaryotes. Proc Natl Acad Sci USA 98: 8714-8719.
19. Kimura M (1983). The Neutral Theory of Evolution. Cambridge University Press: Cambridge, UK.
20. Koonin EV, Ilyina TV (1992). Geminivirus replication proteins are related to prokaryotic plasmid rolling circle DNA-replication initiator proteins. J Gen Virol 73: 2763-2766.
21. Kovarik A, Koukalova B, Lim KY, Matyasek R, Lichtenstein CP, Leitch AR et al (2000). Comparative analysis of DNA methylation in tobacco heterochromatic sequences. Chromosome Res 8: 527-541.
22. Kovarik A, Matyasek R, Leitch A, Gazdova B, Fulnecek J, Bezdek M (1997). Variability in CpNpG methylation in higher plant genomes. Gene 204: 25-33.
23. Lim KY, Matyasek R, Lichtenstein CP, Leitch AR (2000). Molecular cytogenetic analyses and phylogenetic studies in the Nicotiana section Tomentosae. Chromosoma 109: 245-258.
24. Murad L, Lim KY, Christopodulou V, Matyasek R, Lichtenstein CP, Kovarik A (2002). The origin of tobacco's T genome is traced to a particular lineage within Nicotiana tomentosiformis (Solanaceae). Am J Bot 89: 921-928.
25. Penny D, Hendy MD (1985). Testing methods of evolutionary tree construction. Cladistics 1: 266-272.
26. Swofford DL (1993). PAUP: Phylogenetic Analysis using Parsimony. version 3.1.1 Computer Programme. Illinois Natural History Survey: Champaign, IL.
27. Yang ZH (1994). Statistical properties of the maximum-like-lihood method of phylogenetic estimation and comparison with distance matrix-methods. Syst Biol 43: 329-342.
28. Yang ZH (1997). PAML: a program package for phylogenetic analysis by maximum likelihood. Computer Applications in the Biosciences 13: 555-556.
29. Yang Z, Bielawski JP (2000). Statistical methods for detecting molecular adaptation. Trends in Ecology and Evolution 15: 496-503.
30. Yang ZH, Nielsen R (2000). Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 17: 32-43.
31. Yoder JA, Walsh CP, Bestor TH (1997). Cytosine methylation and the ecology of intragenomic parasites. Trends Genet 13: 335-340.
32. Zingg JM, Shen JC, Jones PA (1998). Enzyme-mediated cytosine deamination by the bacterial methyltransferase M.MspI. Biochem J 332: 223-230.