Multiple Origins and nrDNA Internal Transcribed Spacer Homeologue Evolution in the Glycine tomentella (Leguminosae) Allopolyploid Complex

Genetics

Volumn 166, Issue 2, 2004, Pages 987-998

  Rauscher, Jason T ^a,c   Doyle, Jeff J ^a   Brown, A H D ^b  

^a Department of Obstetrics Gynecology   (United States)

^b CSIRO   (Australia)

^c UNIVERSIDAD DE LOS ANDES   (Colombia)

Author keywords

[No Author keywords available]

Indexed keywords

CELL NUCLEUS DNA; INTERNAL TRANSCRIBED SPACER; REPETITIVE DNA;

ALLOPOLYPLOIDY; ARTICLE; DNA MICROARRAY; EVOLUTION; GENE INTERACTION; GENE LOCUS; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GLYCINE TOMENTELLA; LEGUME; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENETICS; PRIORITY JOURNAL; RACE; SEQUENCE HOMOLOGY;

EVOLUTION, MOLECULAR; FABACEAE; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYPLOIDY; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY;

EMBRYOPHYTA; FABACEAE; GLYCINE TOMENTELLA; TOMENTELLA;

EID: 1642413120     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.166.2.987     Document Type: Article

References (44)

1. BALDWIN, B. G., M. J. SANDERSON, J. M. PORTER, M. F. WOJCIECHOWSKI, C. S. CAMPBELL et al., 1995 The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. Ann. Mo. Bot. Gard. 82: 247-277.
2. BRETAGNOLLE, F., F. FELBER, F. G. CALAME and P. KUPFER, 1998 Polyploidy in plants. Bot. Helv. 108: 5-37.
3. BROWN, A. H. D., J. L. DOYLE, J. P. GRACE and J. J. DOYLE, 2002 Molecular phylogenetic relationships within and among diploid races of Glycine tomentella (Leguminosae). Aust. Syst. Bot. 15: 37-47.
4. BUCKLER, E. S., A. IPPOLITO and T. P. HOLTSFORD, 1997 The evolution of ribosomal DNA: divergent paralogues and phylogenetic implications. Genetics 145: 821-832.
5. CHEN, Z. J., L. COMAI and C. S. PIKAARD, 1998 Gene dosage and stochastic effects determine the severity and direction of uniparental rRNA gene silencing (nucleolar dominance) in Arabidopsis allopolyploids. Proc. Natl. Acad. Sci. USA 95: 14891-14896.
6. CLEMENT, M., D. POSADA and K. A. CRANDALL, 2000 TCS: a computer program to estimate gene genealogies. Mol. Ecol. 9: 1657-1659.
7. COOK, L. M., P. S. SOLTIS, S. G. BRUNSFELD and D. E. SOLTIS, 1998 Multiple independent formations of Tragopogon tetraploids (Asteraceae): evidence from RAPD markers. Mol. Ecol. 7: 1293-1302.
8. CRANDALL, K. A., 1994 Intraspecific cladogram estimation-accuracy at higher levels of divergence. Syst. Biol. 43: 222-235.
9. DOYLE, J. J., and A. H. D. BROWN, 1989 5S nuclear ribosomal gene variation in the Glycine tomentella polyploid complex (Leguminosae). Syst. Bot. 14: 398-407.
10. DOYLE, J. J., J. L. DOYLE and A. H. D. BROWN, 1999 Origins, colonization, and lineage recombination in a widespread perennial soybean polyploid complex. Proc. Natl. Acad. Sci. USA 96: 10741-10745.
11. DOYLE, J. J., J. L. DOYLE, A. H. D. BROWN and R. G. PALMER, 2002 Genomes, multiple origins, and lineage recombination in the Glycine tomentella (Leguminosae) polyploid complex: histone H3-D gene sequences. Evolution 56: 1388-1402.
12. DOYLE, M. J., and A. H. D. BROWN, 1985 Numerical analysis of isozyme variation in Glycine tomentella. Biochem. Syst. Ecol. 13: 413-419.
13. DOYLE, M. J., J. E. GRANT and A. H. D. BROWN, 1986 Reproductive isolation between isozyme groups of Glycine tomentella (Leguminosae), and spontaneous doubling in their hybrids. Aust. J. Bot. 34: 523-535.
14. HAMBY, R. K., and E. A. ZIMMER, 1992 Ribosomal RNA as a phylogenetic tool in plant systematics, pp. 50-91 in Molecular Systematics of Plants, edited by P. S. SOLTIS, D. E. SOLTIS and J. J. DOYLE. Chapman & Hall, New York.
15. HSING, Y. C., J.-S. HSIEH, C.-I. PENG, C.-H. CHOU and T.-Y. CHIANG, 2001 Systematic status of the Glycine tomentella and G. tabacina species complexes (Fabaceae) based on ITS sequences of nuclear ribosomal DNA. J. Plant Res. 114: 435-442.
16. HUGHES, C. E., C. D. BAILEY and S. A. HARRIS, 2002 Divergent and reticulate species relationships in Leucaena (Fabaceae) inferred from multiple data sources: insights into polyploid origins and nrDNA polymorphism. Am. J. Bot. 89: 1057-1073.
17. KOLLIPARA, K. P., R. J. SINGH and T. HYMOWITZ, 1994 Genomic diversity and multiple origins of tetraploid (2n=78, 80) Glycine tomentella. Genome 37: 448-459.
18. KOLLIPARA, K. P., R. J. SINGH and T. HYMOWITZ, 1997 Phylogenetic and genomic relationships in the genus Glycine Willd, based on sequences from the ITS region of nuclear nrDNA. Genome 40: 57-68.
19. KRISHNAN, P., V. T. SAPRA, K. M. SOLIMAN and A. ZIPF, 2001 FISH mapping of the 5S and 18S-28S nrDNA loci in different species of Glycine. J. Hered. 92: 295-300.
20. LEE, H. S., and Z. J. CHEN, 2001 Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proc. Natl. Acad. Sci. USA 98: 6753-6758.
21. LEITCH, I. J., and M. D. BENNETT, 1997 Polyploidy in angiosperms. Trends Pharmacol. Sci. 2: 470-476.
22. LEWIS, M. S., and C. S. PIKAARD, 2001 Restricted chromosomal silencing in nucleolar dominance. Proc. Natl. Acad. Sci. USA 98: 14536-14540.
23. MADDISON, W. P., and D. R. MADDISON, 1992 MacClade. Sinauer Associates, Sunderland, MA.
24. OSBORN, T. C., J. C. PIRES, J. A. BIRCHLER, D. L. AUGER, Z. J. CHEN et al., 2003 Understanding mechanisms of novel gene expression in polyploids. Trends Genet. 19: 141-147.
25. PIKAARD, C. S., 2000 The epigenetics of nucleolar dominance. Trends Genet. 16: 675-677.
26. PIKAARD, C. S., 2001 Genomic change and gene silencing in polyploids. Trends Genet. 17: 675-677.
27. RAMBAUT, A., 1995 Se-Al. Sequence Alignment Program. University of Oxford, Oxford.
28. RAUSCHER, J. T., J. J. DOYLE and A. H. D. BROWN, 2002 Internal transcribed spacer repeat-specific primers and the analysis of hybridization in the Glycine tomentella (Leguminosae) polyploid complex. Mol. Ecol. 11: 2691-2702.
29. SANG, T., D. J. CRAWFORD and T. F. STUESSY, 1995 Documentation of reticulate evolution in peonies (Peonia) using internal transcribed spacer sequences of nuclear ribosomal DNA: implications for biogeography and concerted evolution. Proc. Natl. Acad. Sci. USA 92: 6813-6817.
30. SEGRAVES, K. A., J. N. THOMPSON, P. S. SOLTIS and D. E. SOLTIS, 1999 Multiple origins of polyploidy and the geographic structure of Heuchera grossulariifolia. Mol. Ecol. 8: 253-262.
31. SINGH, R. J., K. P. KOLLIPARA and T. HYMOWITZ, 1987 Polyploid complexes of Glycine tabacina (Labill.) Benth. and G. tomentella Hayata revealed by cytogenetic analysis. Genome 29: 490-497.
32. SINGH, R. J., H. H. KIM and T. HYMOWITZ, 2001 Distribution of nrDNA loci in the genus Glycine Willd. Theor. Appl. Genet. 103: 212-218.
33. SOLTIS, D. E., and P. S. SOLTIS, 1991 Multiple origins of the allotetraploid Tragopogon mirus (Compositae): nrDNA evidence. Syst. Bot. 16: 407-413.
34. SOLTIS, D. E., and P. S. SOLTIS, 1999 Polyploidy: recurrent formation and genome evolution. Trends Ecol. Evol. 14: 348-352.
35. SONG, K., P. LU, K. TANG and T. C. OSBORN, 1995 Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proc. Natl. Acad. Sci. USA 92: 7719-7723.
36. SWOFFORD, D. L., 2000 PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods). Sinauer Associates, Sunderland, MA.
37. TEMPLETON, A. R., K. A. CRANDALL and C. F. SING, 1992 A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132: 619-633.
38. TREWICK, S. A., M. MORGAN-RICHARDS, S. J. RUSSELL, S. HENDERSON, F. J. RUMSEY et al., 2002 Polyploidy, phylogeography and Pleistocene refugia of the rockfern Asplenium ceterach: evidence from chloroplast DNA. Mol. Ecol. 11: 2003-2012.
39. TSIGENOPOULOS, C. S., P. RÁB, D. NARAN and P. BERREBI, 2002 Multiple origins of polyploidy in the phylogeny of southern African barbs (Cyprinidae) as inferred from mtDNA markers. Heredity 88: 466-473.
40. VASQUEZ, M. L., 2001 Molecular and morphological studies on Mexican red oaks (Quercus sect. Lobatae). Ph.D. Thesis, Cornell University, Ithaca, NY.
41. WAGNER, A., N. BLACKSTONE, P. CARTWRIGHT, M. DICK, B. MISOF et al., 1994 Surveys of gene families using polymerase chain-reaction-PCR selection and PCR drift. Syst. Biol. 43: 250-261.
42. WENDEL, J. F., 2000 Genome evolution in polyploids. Plant Mol. Biol. 42: 225-249.
43. WENDEL, J. F., A. SCHNABEL and T. SEELANAN, 1995 Bi-directional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proc. Natl. Acad. Sci. USA 92: 280-284.
44. WHITE, T. J., T. BRUNS, S. LEE and J. TAYLOR, 1990 Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenies, pp. 315-322 in PCR Protocols, edited by M. A. INNIS, D. H. GELFAND, J. J. SNINSKY and T. J. WHITE. Academic Press, San Diego.