The flowering world: a tale of duplications

Trends in Plant Science

Volumn 14, Issue 12, 2009, Pages 680-688

  Van de Peer, Yves ^a,b   Fawcett, Jeffrey A ^a,b   Proost, Sebastian ^a,b   Sterck, Lieven ^a,b   Vandepoele, Klaas ^a,b  

^a DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^b GHENT UNIVERSITY   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

ANGIOSPERM; BIOLOGICAL MODEL; CLASSIFICATION; GENE DUPLICATION; GENETICS; MOLECULAR EVOLUTION; PHYLOGENY; PLANT GENOME; POLYPLOIDY; REVIEW; TIME;

ANGIOSPERMS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENOME, PLANT; MODELS, GENETIC; PHYLOGENY; POLYPLOIDY; TIME FACTORS;

MAGNOLIOPHYTA;

EID: 70549110074     PISSN: 13601385     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tplants.2009.09.001     Document Type: Review

References (61)

1. Friis E.M., et al. Cretaceous angiosperm flowers: innovation and evolution in plant reproduction. Palaeogeogr. Palaeocl. 232 (2006) 251-293
2. Moore M.J., et al. Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms. Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 19363-19368
3. Crepet W.L., and Niklas K.J. Darwin's second "abominable mystery": why are there so many angiosperm species?. Amer. J. Bot. 96 (2009) 366-381
4. De Bodt S., et al. Genome duplication and the origin of angiosperms. Trends Ecol. Evol. 20 (2005) 591-597
5. Soltis D.E., et al. Polyploidy and angiosperm diversification. Am. J. Bot. 96 (2009) 336-348
6. Freeling M. Bias in plant gene content following different sorts of duplication: tandem, whole-genome segmental, or by transposition. Annu. Rev. Plant. Biol. 60 (2009) 433-453
7. Bowers J.E., et al. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422 (2003) 433-438
8. Simillion C., et al. The hidden duplication past of Arabidopsis thaliana. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 13627-13632
9. Zahn L.M., et al. The evolution of the SEPALLATA subfamily of MADS-box genes: a preangiosperm origin with multiple duplications throughout angiosperm history. Genetics 169 (2005) 2209-2223
10. Maere S., et al. Modeling gene and genome duplications in eukaryotes. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 5454-5459
11. Veron A.S., et al. Evidence of interaction network evolution by whole-genome duplications: a case study in MADS-box proteins. Mol. Biol. Evol. 24 (2007) 670-678
12. Jaillon O., et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449 (2007) 463-467
13. Ming R., et al. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452 (2008) 991-996
14. Wikström N., et al. Evolution of the angiosperms: calibrating the family tree. Proc. R Soc. Lond. B 268 (2001) 2211-2220
15. Jansen R.K., et al. Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evol. Biol. 6 (2006) 32
16. Jansen R.K., et al. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 19369-19374
17. Tang H., et al. Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res. 18 (2008) 1944-1954
18. Velasco R., et al. A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS ONE 2 (2007) e1326
19. Paterson A.H., et al. Ancient duplication of cereal genomes. New Phytol. 165 (2005) 658-661
20. Zhang Y., et al. Two ancient rounds of polyploidy in rice genome. J. Zhejiang Univ. Sci. 6B (2005) 87-90
21. Vandepoele K., et al. Evidence that rice and other cereals are ancient aneuploids. Plant Cell 15 (2003) 2192-2202
22. Cui L., et al. Widespread genome duplications throughout the history of flowering plants. Genome Res. 16 (2006) 738-749
23. Bell C.D., et al. The age of the angiosperms: a molecular timescale without a clock. Evolution 59 (2005) 1245-1258
24. Barker M.S., et al. Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years. Mol. Biol. Evol. 25 (2008) 2445-2455
25. Lyons E., et al. The value of nonmodel genomes and an example using SynMap within CoGe to dissect the hexaploidy that predates the rosids. Tropical Plant Biol. 1 (2008) 181-190
26. Blanc G., and Wolfe K.H. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16 (2004) 1667-1678
27. Schlueter J.A., et al. Mining EST databases to resolve evolutionary events in major crop species. Genome 47 (2004) 868-876
28. Lescot M., et al. Insights into the Musa genome: syntenic relationships to rice and between Musa species. BMC Genomics 9 (2008) 58
29. Fawcett J.A., et al. Plants with double genomes might have had a better chance to survive the Cretaceous- Tertiary extinction event. Proc. Natl. Acad. Sci. U. S. A. 106 (2009) 5737-5742
30. Tuskan G.A., et al. The genome of black cottonwood. Populus trichocarpa (Torr. & Gray). Science 313 (2006) 1596-1604
31. Paterson A.H., et al. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 9903-9908
32. Soltis D.E., and Burleigh J.G. Surviving the K-T mass extinction: new perspectives of polyploidization in angiosperms. Proc. Natl. Acad. Sci. U. S. A. 106 (2009) 5455-5456
33. Freeling M., et al. Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Res. 18 (2008) 1924-1937
34. Vandepoele K., et al. Detecting the undetectable: uncovering duplicated segments in Arabidopsis by comparison with rice. Trends Genet. 18 (2002) 606-608
35. Van de Peer Y. Computational approaches to unveiling ancient genome duplications. Nat. Rev. Genet. 5 (2004) 752-763
36. Tang H., et al. Synteny and collinearity in plant genomes. Science 320 (2008) 486-488
37. Simillion C., et al. Building genomic profiles for uncovering segmental homology in the twilight zone. Genome Res. 14 (2004) 1095-1106
38. Soltis P.S., and Soltis D.E. The role of hybridization in plant speciation. Annu. Rev. Plant Biol. 60 (2009) 561-588
39. Thomas B.C., et al. Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res. 16 (2006) 934-946
40. Zheng C., et al. Gene loss under neighborhood selection following whole genome duplication and the reconstruction of the ancestral Populus genome. J. Bioinform. Comput. Biol. 7 (2009) 499-520
41. Cannon S.B., et al. Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 14959-14964
42. Pfeil B.E., et al. Placing paleopolyploidy in relation to taxon divergence: a phylogenetic analysis in legumes using 39 gene families. Syst. Biol. 54 (2005) 441-454
43. Van de Peer Y., et al. Dealing with saturation at the amino acid level: a case study based on anciently duplicated zebrafish genes. Gene 295 (2002) 205-211
44. Van de Peer Y., et al. The evolutionary significance of ancient genome duplications. Nat. Rev. Genet. 10 (2009) 725-732
45. Bowman J.L., et al. Green genes-comparative genomics of the green branch of life. Cell 129 (2007) 229-234
46. Soltis D.E., et al. Origin and early evolution of angiosperms. Ann. NY Acad. Sci. 1133 (2008) 3-25
47. Swarbreck D., et al. The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res. 36 (2008) D1009-1014
48. Sato S., et al. Genome Structure of the Legume. Lotus japonicus. DNA Res. 15 (2008) 227-239
49. Sterck L., et al. How many genes are there in plants (... and why are they there)?. Curr. Opin. Plant Biol. 10 (2007) 199-203
50. Tanaka T., et al. The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res. 36 (2008) D1028-1033
51. Vandepoele K., and Van de Peer Y. Exploring the plant transcriptome through phylogenetic profiling. Plant Phys. 137 (2005) 31-42
52. Seoighe C., and Gehring C. Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome. Trends Genet. 20 (2004) 461-464
53. Blanc G., and Wolfe K.H. Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16 (2004) 1679-1691
54. Chapman B.A., et al. Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 2730-2735
55. Schranz M.E., and Mitchell-Olds T. Independent ancient polyploidy events in the sister families Brassicaceae and Cleomaceae. Plant Cell 18 (2006) 1152-1165
56. Blomme T., et al. The gain and loss of genes during 600 million years of vertebrate evolution. Genome Biol. 7 (2006) R43
57. Davis J.C., and Petrov D.A. Do disparate mechanisms of duplication add similar genes to the genome?. Trends Genet. 21 (2005) 548-551
58. Freeling M., and Thomas B.C. Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Res. 16 (2006) 805-814
59. Papp B., et al. Dosage sensitivity and the evolution of gene families in yeast. Nature 424 (2003) 194-197
60. Krylov D.M., et al. Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res. 13 (2003) 2229-2235
61. Simillion C., et al. i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles. Bioinformatics 24 (2008) 127-128