Evolution and expression of homeologous loci in Tragopogon miscellus (Asteraceae), a recent and reciprocally formed allopolyploid

Genetics

Volumn 173, Issue 3, 2006, Pages 1599-1611

  Tate, Jennifer A ^a,e   Ni, Zhongfu ^b   Scheen, Anne Cathrine ^c   Koh, Jin ^a   Gilbert, Candace A ^a   Lefkowitz, David ^a   Chen, Z Jeffrey ^b   Soltis, Pamela S ^d   Soltis, Douglas E ^a  

^a UNIVERSITY OF FLORIDA   (United States)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^c UNIVERSITY OF OSLO   (Norway)

^d UNIVERSITY OF FLORIDA   (United States)

^e MASSEY UNIVERSITY   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

ALLOPOLYPLOIDY; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; ASTERACEAE; CLEAVED AMPLIFIED POLYMORPHIC SEQUENCE; CONTROLLED STUDY; DNA POLYMORPHISM; GENE DUPLICATION; GENE EXPRESSION; GENE LOCUS; NONHUMAN; POLYPLOIDY; PRIORITY JOURNAL; TRAGOPOGON;

DIPLOIDY; DNA, COMPLEMENTARY; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, PLANT; GENETICS, POPULATION; GENOME, PLANT; HYBRIDIZATION, GENETIC; MOLECULAR SEQUENCE DATA; POLYMORPHISM, SINGLE-STRANDED CONFORMATIONAL; POLYPLOIDY; SEEDS; TRAGOPOGON;

ASTERACEAE; TRAGOPOGON; TRAGOPOGON DUBIUS; TRAGOPOGON MISCELLUS; TRAGOPOGON PRATENSIS;

EID: 33746424003     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.106.057646     Document Type: Article

References (61)

1. ADAMS, K. L., R. C. CRONN, R. PERCIFIELD and J. F. WENDEL, 2003 Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc. Natl. Acad. Sci. USA 100: 4649-4654.
2. ADAMS, K. L., R. PERCIFIELD and J. F. WENDEL, 2004 Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics 168: 2217-2226.
3. BACHEM, C. W. B., R. S. VAN DER HOEVEN, S. M. DE BRUIJN, D. VREUGDENHIL, M. ZABEAU et al., 1996 Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: analysis of gene expression during potato tuber development. Plant J. 9: 745-753.
4. BLANC, G., and K. H. WOLFE, 2004a Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16: 1679-1691.
5. BLANC, G., and K. H. WOLFE, 2004b Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16: 1667-1678.
6. BLANC, G., K. HOKAMP and K. H. WOLFE, 2003 A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res. 13: 137-144.
7. BOWERS, J. E., B. A. CHAPMAN, J. RONG and A. H. PATERSON, 2003 Unraveling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422: 433-438.
8. BREHM, B. G., and M. OWNBEY, 1965 Variation in chromatographic patterns in the Tragopogon dubius-pratensis-porrifolius complex (Compositae). Am. J. Bot. 52: 811-818.
9. CHEN, Z. J., and Z. NI, 2006 Mechanisms of genomic rearrangements and gene expression changes in plant polyploids. BioEssays 28: 240-252.
10. COMAI, L., A. P. TYAGI, K. WINTER, R. HOLMES-DAVIS, S. H. REYNOLDS et al., 2000 Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids. Plant Cell 12: 1551-1567.
11. COOK, L. M., P. S. SOLTIS, S. J. BRUNSFELD and D. E. SOLTIS, 1998 Multiple independent formations of Tragopogon tetraploids (Asteraceae): evidence from RAPD markers. Mol. Ecol. 7: 1293-1302.
12. DOYLE, J. J., and J. L. DOYLE, 1987 A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19: 11-15.
13. FAHSELT, D., M. OWNBEY and M. BORTON, 1976 Seed fertility in Tragopogon hybrids (Compositae). Am. J. Bot. 63: 1109-1118.
14. FELDMAN, M., B. LIU, G. SEGAL, S. ABBO, A. A. LEVY et al., 1997 Rapid elimination of low-copy DNA sequences in polyploid wheat: a possible mechanism for differentiation of homoeologous chromosomes. Genetics 147: 1381-1387.
15. GRANT, V., 2002 Frequency of spontaneous amphiploids in Gilia (Polemoniaceae) hybrids. Am. J. Bot. 89: 1197-1202.
16. HARRIS, J. I., and M. WATER, 1976 Glyceraldehyde-3-phosphate dehydrogenase, pp. 1-49 in The Enzymes, edited by P. D. BOYER. Academic Press, New York.
17. HE, P., B. R. FRIEBE, B. S. GILL and J.-M. ZHOU, 2003 Allopolyploidy alters gene expression in the highly stable hexaploid wheat. Plant Mol. Biol. 52: 401-414.
18. JOLY, S., J. T. RAUSCHER, S. L. SHERMAN-BROYLES, A. H. D. BROWN and J. J. DOYLE, 2004 Evolutionary dynamics and preferential expression of homeologous 18S-5.8S-26S nuclear ribosomal genes in natural and artificial Glycine allopolyploids. Mol. Biol. Evol. 21: 1409-1421.
19. KASHKUSH, K., M. FELDMAN and A. A. LEVY, 2002 Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics 160: 1651-1659.
20. KASHKUSH, K., M. FELDMAN and A. A. LEVY, 2003 Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat. Genet. 33: 102-106.
21. KONIECZNY, A., and F. M. AUSUBEL, 1993 A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J. 4: 403-410.
22. KOVARÍK, A., J. C. PIRES, A. R. LEITCH, K. Y. LIM, A. SHERWOOD et al., 2005 Rapid concerted evolution of nuclear ribosomal DNA in two Tragopogon allopolyploids of recent and recurrent origin. Genetics 169: 931-944.
23. 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.
24. LEITCH, I. J., and M. D. BENNETT, 1997 Polyploidy in angiosperms. Trends Plant Sci. 2: 470-476.
25. LEITCH, I. J., and M. D. BENNETT, 2004 Genome downsizing in polyploid plants. Biol. J. Linn. Soc. 82: 651-663.
26. LEVIN, D. A., 1983 Polyploidy and novelty in flowering plants. Am. Nat. 122: 1-25.
27. LEVY, A. A., and M. FELDMAN, 2004 Genetic and epigenetic reprogramming of the wheat genome upon allopolyploidization. Biol. J. Linn. Soc. 82: 607-613.
28. LIU, B., and J. F. WENDEL, 2003 Epigenetic phenomena and the evolution of plant allopolyploids. Mol. Phylogenet. Evol. 29: 365-379.
29. LIU, B., J. M. VEGA and M. FELDMAN, 1998 Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. II. Changes in low-copy coding DNA sequences. Genome 41: 535-542.
30. LIU, B., C. L. BRUBAKER, G. MERGEAI, R. C. CRONN and J. F. WENDEL, 2001 Polyploid formation in cotton is not accompanied by rapid genomic changes. Genome 44: 321-330.
31. LUKENS, L., P. QUIJADA, J. UDALL, J. C. PIRES, M. E. SCHRANZ et al., 2004 Genome redundancy and plasticity within ancient and recent Brassica crop species. Biol. J. Linn. Soc. 82: 665-674.
32. LUKENS, L. N., J. C. PIRES, E. J. LEON, R. VOGELZANG, L. OSLACH et al., 2006 Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus allopolyploids. Plant Physiol. 140: 336-348.
33. LYNCH, M., and J. S. CONERY, 2000 The evolutionary fate of duplicated genes. Science 290: 1151-1154.
34. MAVRODIEV, E. V., M. TANCIG, A. M. SHERWOOD, M. A. GITZENDANNER, J. ROCCA et al., 2005 Phylogeny of Tragopogon L. (Asteraceae) based on internal and external transcribed spacer sequence data. Int. J. Plant Sci. 166: 117-133.
35. MCCLINTOCK, B., 1984 The significance of responses of the genome to challenge. Science 226: 792-801.
36. NOVAK, S. J., D. E. SOLTIS and P. S. SOLTIS, 1991 Ownbey's Tragopogons: 40 years later. Am. J. Bot. 78: 1586-1600.
37. OHNO, S., 1970 Evolution by Gene Duplication. Springer-Verlag, New York.
38. 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.
39. OWNBEY, M., 1950 Natural hybridization and amphiploidy in the genus Tragopogon. Am. J. Bot. 37: 487-499.
40. OWNBEY, M., and G. D. MCCOLLUM, 1953 Cytoplasmic inheritance and reciprocal amphiploidy inTragopogon.Am.J. Bot. 40: 788-796.
41. OWNBEY, M., and G. D. MCCOLLUM, 1954 The chromosomes of Tragopogon. Rhodora 56: 7-21.
42. OZKAN, H., A. A. LEVY and M. FELDMAN, 2001 Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops-Triticum) group. Plant Cell 13: 1735-1747.
43. PIRES, J. C., K. Y. LIM, A. KOVARÍK, R. MATYÁSEK, A. BOYD et al., 2004a Molecular cytogenetic analysis of recently evolved Tragopogon (Asteraceae) allopolyploids reveals a karyotype that is additive of the diploid progenitors. Am. J. Bot. 91: 1022-1035.
44. PIRES, J. C., J. ZHAO, M. E. SCHRANZ, E. J. LEON, P. A. QUIJADA et al., 2004b Flowering time divergence and genomic rearrangements in resynthesized polyploids (Brassica). Biol. J. Linn. Soc. 82: 675-688.
45. PRINCE, V. E., and F. B. PICKETT, 2002 Splitting pairs: the diverging fates of duplicated genes. Nat. Rev. Genet. 3: 827-837.
46. ROOSE, M. L., and L. D. GOTTLIEB, 1976 Genetic and biochemical consequences of polyploidy in Tragopogon. Evolution 30: 818-830.
47. ROZEN, S., and H. J. SKALETSKY, 1997 Primer3. http://frodo.wi.mit. edu/cgi-bin/primer3/primer3_www.cgi.
48. SALMON, A., M. L. AINOUCHE and J. F. WENDEL, 2005 Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Mol. Ecol. 14: 1163-1175.
49. SHAKED, H., K. KASHKUSH, H. OZKAN, M. FELDMAN and A. A. LEVY, 2001 Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 13: 1749-1759.
50. SOLTIS, D. E., and P. S. SOLTIS, 1989 Allopolyploid speciation in Tragopogon: insights from chloroplast DNA. Am. J. Bot. 76: 1119-1124.
51. SOLTIS, D. E., and P. S. SOLTIS, 1993 Molecular data and the dynamic nature of polyploidy. Crit. Rev. Plant Sci. 12: 243-273.
52. SOLTIS, D. E., and P. S. SOLTIS, 1999 Polyploidy: recurrent formation and genome evolution. Trends Ecol. Evol. 14: 348-352.
53. SOLTIS, P. S., G. M. PLUNKETT, S. J. NOVAK and D. E. SOLTIS, 1995 Genetic variation in Tragopogon species: additional origins of the allotetraploids T. mirus and T. miscellus (Compositae). Am. J. Bot. 82: 1329-1341.
54. SOLTIS, D. E., P. S. SOLTIS, J. C. PIRES, A. KOVARÍK, J. A. TATE et al., 2004 Recent and recurrent polyploidy in Tragopogon (Asteraceae): cytogenetic, genomic, and genetic comparisons. Biol. J. Linn. Soc. 82: 485-501.
55. 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.
56. STEBBINS, G. L., 1950 Variation and Evolution in Plants. Columbia University Press, New York.
57. VISION, T. J., D. G. BROWN and S. D. TANKSLEY, 2000 The origins of genomic duplications in Arabidopsis. Science 290: 2114-2117.
58. WANG, J., L. TIAN, A. MADLUNG, H.-S. LEE, M. CHEN et al., 2004 Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics 167: 1961-1973.
59. WANG, J., J. J. LEE, H.-S. LEE, M. CHEN, S. RAO et al., 2005 Methods for genome-wide analysis of gene expression changes in polyploids. Methods Enzymol. 395: 570-596.
60. WENDEL, J. F., 2000 Genome evolution in polyploids. Plant Mol. Biol. 42: 225-249.
61. ZHAO, X.-P., Y. SI, R. E. HANSON, C. F. CRANE, H. J. PRICE et al., 1998 Dispersed repetitive DNA has spread to new genomes since polyploid formation in cotton. Genome Res. 8: 479-492.