Ancient whole genome duplications, novelty and diversification: The WGD Radiation Lag-Time Model

Current Opinion in Plant Biology

Volumn 15, Issue 2, 2012, Pages 147-153

  Eric Schranz, M ^a   Mohammadin, Setareh ^a   Edger, Patrick P ^b  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

^b UNIVERSITY OF MISSOURI   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLASSIFICATION; GENE DUPLICATION; GENETICS; MOLECULAR EVOLUTION; PLANT; PLANT GENOME; REVIEW; THEORETICAL MODEL;

EVOLUTION, MOLECULAR; GENE DUPLICATION; GENOME, PLANT; MODELS, THEORETICAL; PLANTS;

ASTERACEAE; BRASSICACEAE; FABACEAE; POACEAE; SOLANACEAE;

EID: 84859917501     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbi.2012.03.011     Document Type: Review

References (73)

1. Winge Ø. The chromosomes: their numbers and general importance. Compt rend trav lab Carlsberg 1917, 13:131-275.
2. Edger P.P., Pires J.C. Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes. Chromosome Res 2009, 17:699-717.
3. Muffato M., Crollius H.R. Paleogenomics in vertebrates, or the recovery of lost genomes from the mist of time. Bioessays 2008, 30:122-134.
4. Scannell D.R., Byrne K.P., Gordon J.L., Wong S., Wolfe K.H. Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature 2006, 440:341-345.
5. Hoegg S., Brinkmann H., Taylor J.S., Meyer A. Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish. J Mol Evol 2004, 59:190-203.
6. Van de Peer Y., Maere S., Meyer A. OPINION: The evolutionary significance of ancient genome duplications. Nat Rev Genet 2009, 10:725-732.
7. Ihmels J., Bergmann S., Gerami-Nejad M., Yanai I., McClellan M., Berman J., Barkai N. Rewiring of the yeast transcriptional network through the evolution of motif usage. Science 2005, 309:938-940.
8. Braasch I., Schartl M., Volff J. Evolution of pigment synthesis pathways by gene and genome duplication in fish. BMC Evol Biol 2007, 7:74.
9. Ohno S. Evolution by Gene Duplication 1970, Springer-Verlag.
10. Soltis D.E., Albert V.A., Leebens-Mack J., Bell C.D., Paterson A.H., Zheng C.F., Sankoff D., dePamphilis C.W., Wall P.K., Soltis P.S. Polyploidy and angiosperm diversification. Am J Bot 2009, 96:336-348.
11. Semon M., Wolfe K.H. Reciprocal gene loss between Tetraodon and zebrafish after whole genome duplication in their ancestor. Trends Genet 2007, 23:108-112.
12. Thomas B.C., Pedersen B., Freeling M. Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res 2006, 16:934-946.
13. Sankoff D., Zheng C., Wang B. A model for biased fractionation after whole genome duplication. BMC Genomics 2012, 13(Suppl. 1):S8.
14. Santini F., Harmon L.J., Carnevale G., Alfaro M.E. Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes. BMC Evol Biol 2009, 9:194.
15. Luo Z., Yuan C., Meng Q., Ji Q. A Jurassic eutherian mammal and divergence of marsupials and placentals. Nature 2011, 476:442-445.
16. Erwin D.H., Laflamme M., Tweedt S.M., Sperling E.A., Pisani D., Peterson K.J. The Cambrian Conundrum: early divergence and later ecological success in the early history of animals. Science 2011, 334:1091-1097.
17. Doyle J.J., Luckow M.A. The rest of the iceberg. Legume diversity and evolution in a phylogenetic context. Plant Physiol 2003, 131:900-910.
18. Jiao Y., Leebens-Mack J., Ayyampalayam S., Bowers J.E., McKain M.R., McNeal J., Rolf M., Ruzicka D.R., Wafula E., Wickett N.J., et al. A genome triplication associated with early diversification of the core eudicots. Genome Biology 2012, 13:R3. 10.1186/gb-2012-13-1-r3.
19. Fawcett J.A., Maere S., Van de Peer Y. Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Proc Natl Acad Sci U S A 2009, 106:5737-5742.
20. Jiao Y., Wickett N.J., Ayyampalayam S., Chanderbali A.S., Landherr L., Ralph P.E., Tomsho L.P., Hu Y., Liang H., Soltis P.S., et al. Ancestral polyploidy in seed plants and angiosperms. Nature 2011, 473:U97-U113.
21. Smith S.A., Donoghue M.J. Rates of molecular evolution are linked to life history in flowering plants. Science 2008, 322:86-89.
22. Soltis D.E., Albert V.A., Leebens-Mack J., Bell C.D., Paterson A.H., Zheng C., Sankoff D., dePamphilis C.W., Wall P.K., Soltis P.S. Polyploidy and angiosperm diversification. Am J Bot 2009, 96:336-348.
23. Van de Peer Y., Fawcett J.A., Proost S., Sterck L., Vandepoele K. The flowering world: a tale of duplications. Trends Plant Sci 2009, 14:680-688.
24. Stevens PF. Angiosperm Phylogeny Website 2001, onwards.
25. Wood T.E., Takebayashi N., Barker M.S., Mayrose I., Greenspoon P.B., Rieseberg L.H. The frequency of polyploid speciation in vascular plants. Proc Natl Acad Sci U S A 2009, 106:13875-13879.
26. Smith S.A., Beaulieu J.M., Stamatakis A., Donoghue M.J. Understanding angiosperm diversification using small and large phylogenetic trees. Am J Bot 2011, 98:404-414.
27. Glor R.E. Phylogenetic insights on adaptive radiation. Annu Rev Ecol Evol Syst 2010, 41:251-270.
28. Crisp M.D., Cook L.G. Do early branching lineages signify ancestral traits?. Trends Ecol Evol 2005, 20:122-128.
29. Arrigo N., Barker M.S. Rarely successful polyploids and their legacy in plant genomes. Curr Opin Plant Biol 2012, this issue. 10.1016/j.pbi.2012.03.010.
30. Schranz M.E., Mitchell-Olds T. Independent ancient polyploidy events in the sister families Brassicaceae and Cleomaceae. Plant Cell 2006, 18:1152-1165.
31. Couvreur T.L.P., Franzke A., Al-Shehbaz I.A., Bakker F.T., Koch M.A., Mummenhoff K. Molecular phylogenetics, temporal diversification, and principles of evolution in the mustard family (Brassicaceae). Mol Biol Evol 2010, 27:55-71.
32. Ansell S.W., Stenoien H.K., Grundmann M., Russell S.J., Koch M.A., Schneider H., Vogel J.C. The importance of Anatolian mountains as the cradle of global diversity in Arabis alpina, a key arctic-alpine species. Ann Bot 2011, 108:241-252.
33. Al-Shehbaz I.A., Beilstein M.A., Kellogg E.A. Systematics and phylogeny of the Brassicaceae (Cruciferae): an overview. Plant Syst Evol 2006, 259:89-120.
34. Woodhouse M.R., Tang H., Freeling M. Different gene families in Arabidopsis thaliana transposed in different epochs and at different frequencies throughout the rosids. Plant Cell 2011, 23:4241-4253.
35. Moore R.C., Grant S.R., Purugganan M.D. Molecular population genetics of redundant floral-regulatory genes in Arabidopsis thaliana. Mol Biol Evol 2005, 22:91-103.
36. Schranz M.E., Edger P.P., Pires J.C., van Dam N.M., Wheat C.W. Comparative genomics in the Brassicales: ancient genome duplications, glucosinolate diversification and pierinae herbivore radiation. Genetics, Genomics and Breeding of Oilseed Brassicas 2011, 219-229. CRC Press. D.P.I. Edwards, J. Batley (Eds.).
37. Barker M.S., Kane N.C., Matvienko M., Kozik A., Michelmore W., Knapp S.J., Rieseberg L.H. Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years. Mol Biol Evol 2008, 25:2445-2455.
38. Franzke A., Lysak M.A., Al-Shehbaz I.A., Koch M.A., Mummenhoff K. Cabbage family affairs: the evolutionary history of Brassicaceae. Trends Plant Sci 2011, 16:108-116.
39. Beilstein M.A., Nagalingum N.S., Clements M.D., Manchester S.R., Mathews S. Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana. Proc Natl Acad Sci U S A 2010, 107:18724-18728.
40. Preston J.C., Christensen A., Malcomber S.T., Kellogg E.A. Mads-box gene expression and implications for developmental origins of the grass spikelet. Am J Bot 2009, 96:1419-1429.
41. Wu Y., Zhu Z., Ma L., Chen M. The preferential retention of starch synthesis genes reveals the impact of whole-genome duplication on grass evolution. Mol Biol Evol 2008, 25:1003-1006.
42. Bouchenak-Khelladi Y., Verboom G.A., Savolainen V., Hodkinson T.R. Biogeography of the grasses (Poaceae): a phylogenetic approach to reveal evolutionary history in geographical space and geological time. Bot J Linn Soc 2010, 162:543-557.
43. Stroemberg C.A.E. Evolution of grasses and grassland ecosystems. Annu Rev Earth Planet Sci 2011, 39:517-544.
44. Kellogg E.A. Evolutionary history of the grasses. Plant Physiol 2001, 125:1198-1205.
45. Salse J., Bolot S., Throude M., Jouffe V., Piegu B., Quraishi U.M., Calcagno T., Cooke R., Delseny M., Feuillet C. Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. Plant Cell 2008, 20:11-24.
46. Paterson A.H., Bowers J.E., Chapman B.A. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci U S A 2004, 101:9903-9908.
47. Gaut B.S., Peek A.S., Morton B.R., Clegg M.T. Patterns of genetic diversification within the Adh gene family in the grasses (Poaceae). Mol Biol Evol 1999, 16:1086-1097.
48. Barreda V.D., Palazzesi L., Katinas L., Crisci J.V., Telleria M.C., Bremer K., Passala M.G., Bechis F., Corsolini R. An extinct Eocene taxon of the daisy family (Asteraceae): evolutionary, ecological and biogeographical implications. Ann Bot 2012, 109:127-134.
49. Ruokolainen S., Ng Y.P., Albert V.A., Elomaa P., Teeri T.H. Large scale interaction analysis predicts that the Gerbera hybrida floral E function is provided both by general and specialized proteins. BMC Plant Biol 2010, 10:129.
50. Nguyen D.T., Goepfert J.C., Ikezawa N., MacNevin G., Kathiresan M., Conrad J., Spring O., Ro D. Biochemical conservation and evolution of germacrene A oxidase in Asteraceae. J Biol Chem 2010, 285:16588-16598.
51. Gruenstaeudl M., Urtubey E., Jansen R.K., Samuel R., Barfuss M.H.J., Stuessy T.F. Phylogeny of Barnadesioideae (Asteraceae) inferred from DNA sequence data and morphology. Mol Phylogenet Evol 2009, 51:572-587.
52. Panero J.L., Funk V.A. The value of sampling anomalous taxa in phylogenetic studies: major clades of the Asteraceae revealed. Mol Phylogenet Evol 2008, 47:757-782.
53. Kane N.C., Barker M.S., Zhan S.H., Rieseberg L.H. Molecular evolution across the Asteraceae: micro- and macroevolutionary processes. Mol Biol Evol 2011, 28:3225-3235.
54. Tucker S.C. Floral development in legumes. Plant Physiol 2003, 131:911-926.
55. Doyle J.J. Phylogenetic perspectives on the origins of nodulation. Mol Plant Microbe Interact 2011, 24:1289-1295.
56. den Camp R.H.M.O., De Mita S., Lillo A., Cao Q., Limpens E., Bisseling T., Geurts R. A phylogenetic strategy based on a legume-specific whole genome duplication yields symbiotic cytokinin type-A response regulators. Plant Physiol 2011, 157:2013-2022.
57. Sprent J.I. Nodulation in a taxonomic context. Legume Nodulation 2009, 1-33. Wiley-Blackwell. Anonymous (Ed.).
58. Lavin M., Herendeen P.S., Wojciechowski M.F. Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the tertiary. Syst Biol 2005, 54:575-594.
59. Schrire B.D., Lavin M., Lewis G.P. Global distribution patterns of the Leguminosae: insight from recent phylogenies. Plant Diversity and Complexity: Local, Regional and Global Dimensions 2005, 375-415. Special-Trykkeriet Viborg a-s. I. Friis, H. Balslev (Eds.).
60. Bello M.A., Bruneau A., Forest F., Hawkins J.A. Elusive relationships within order fabales: phylogenetic analyses using matK and rbcL sequence data. Syst Bot 2009, 34:102-114.
61. Knapp S. Tobacco to tomatoes: a phylogenetic perspective on fruit diversity in the Solanaceae. J Exp Bot 2002, 53:2001-2022.
62. Pomilio A.B., Falzoni E.M., Vitale A.A. Toxic chemical compounds of the Solanaceae. Nat Prod Commun 2008, 3:593-628.
63. Olmstead R.G., Bohs L., Migid H.A., Santiago-Valentin E., Garcia V.F., Collier S.M. A molecular phylogeny of the Solanaceae. Taxon 2008, 57:1159-1181.
64. Wu F., Tanksley S.D. Chromosomal evolution in the plant family Solanaceae. BMC Genomics 2010, 11:182.
65. Knapp S. On 'various contrivances': pollination, phylogeny and flower form in the Solanaceae. Philos Trans R Soc Lond B Biol Sci 2010, 365:449-460.
66. Kim S., Koh J., Yoo M.J., Kong H.Z., Hu Y., Ma H., Soltis P.S., Soltis D.E. Expression of floral MADS-box genes in basal angiosperms: implications for the evolution of floral regulators. Plant J 2005, 43:724-744.
67. Williams J.H. Amborella trichopoda (Amborellaceae) and the evolutionary developmental origins of the angiosperm progamic phase. Am J Bot 2009, 96:144-165.
68. Soltis D.E., Smith S.A., Cellinese N., Wurdack K.J., Tank D.C., Brockington S.F., Refulio-Rodriguez N.F., Walker J.B., Moore M.J., Carlsward B.S., et al. Angiosperm phylogeny: 17 genes, 640 taxa. Am J Bot 2011, 98:704-730.
69. Soltis D.E., Albert V.A., Leebens-Mack J., Palmer J.D., Wing R.A., dePamphilis C.W., Ma H., Carlson J.E., Altman N., Kim S., et al. The Amborella genome: an evolutionary reference for plant biology. Genome Biol 2008, 9:402.
70. Jolivet P., Verma K.K. Good morning Gondwana. Ann Soc Entomol Fr 2010, 46:53-61.
71. Lee E.K., Cibrian-Jaramillo A., Kolokotronis S., Katari M.S., Stamatakis A., Ott M., Chiu J.C., Little D.P., Stevenson D.W., McCombie W.R., et al. A functional phylogenomic view of the seed plants. PLoS Genet 2011, 7:e1002411.
72. Chanderbali A.S., Yoo M., Zahn L.M., Brockington S.F., Wall P.K., Gitzendanner M.A., Albert V.A., Leebens-Mack J., Altman N.S., Ma H., et al. Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower. Proc Natl Acad Sci U S A 2010, 107:22570-22575.
73. Bertioli D.J., Moretzsohn M.C., Madsen L.H., Sandal N., Leal-Bertioli S.C.M., Guimaraes P.M., Hougaard B.K., Fredslund J., Schauser L., Nielsen A.M., et al. An analysis of synteny of Arachis with Lotus and Medicago sheds new light on the structure, stability and evolution of legume genomes. BMC Genomics 2009, 10:45.