References
Ohno, S. Evolution by Gene Duplication (Springer, 1970)
Lynch, M. The Origins of Genome Architecture (Sinauer, 2007)
Edger, P. P. & Pires, J. C. Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes. Chromosome Res. 17, 699–717 (2009)
De Bodt, S., Maere, S. & Van de Peer, Y. Genome duplication and the origin of angiosperms. Trends Ecol. Evol. 20, 591–597 (2005)
Soltis, D. E., Bell, C. D., Kim, S. & Soltis, P. S. Origin and early evolution of angiosperms. Ann. NY Acad. Sci. 1133, 3–25 (2008)
Article ADS CAS Google Scholar
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. USA 106, 5737–5742 (2009)
Article ADS CAS Google Scholar
Lyons, E. et al. Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiol. 148, 1772–1781 (2008)
Bowers, J. E., Chapman, B. A., Rong, J. & Paterson, A. H. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422, 433–438 (2003)
Article ADS CAS Google Scholar
Jaillon, O. et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449, 463–467 (2007)
Article ADS CAS Google Scholar
Vision, T. J., Brown, D. G. & Tanksley, S. D. The origins of genomic duplications in Arabidopsis . Science 290, 2114–2117 (2000)
Article ADS CAS Google Scholar
Barker, M. S., Vogel, H. & Schranz, M. E. Paleopolyploidy in the Brassicales: analyses of the Cleome transcriptome elucidate the history of genome duplications in Arabidopsis and other Brassicales. Genome Biol. Evol. 1, 391–399 (2009)
Tang, H. et al. Synteny and collinearity in plant genomes. Science 320, 486–488 (2008)
Article ADS CAS Google Scholar
Tang, H. et al. Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res. 18, 1944–1954 (2008)
Tuskan, G. A. et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313, 1596–1604 (2006)
Article ADS CAS Google Scholar
Tang, H., Bowers, J. E., Wang, X. & Paterson, A. H. Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Proc. Natl Acad. Sci. USA 107, 472–477 (2010)
Article ADS CAS Google Scholar
Cui, L. et al. Widespread genome duplications throughout the history of flowering plants. Genome Res. 16, 738–749 (2006)
Blomme, T. et al. The gain and loss of genes during 600 million years of vertebrate evolution. Genome Biol. 7, R43 (2006)
Ebersberger, I., Strauss, S. & von Haeseler, A. HaMStR: profile hidden Markov model based search for orthologs in ESTs. BMC Evol. Biol. 9, 157 (2009)
Moore, M. J., Bell, C. D., Soltis, P. S. & Soltis, D. E. Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms. Proc. Natl Acad. Sci. USA 104, 19363–19368 (2007)
McLachlan, G., Peel, D., Basford, K. E. & Adams, P. The EMMIX algorithm for the fitting of normal and t-components. J. Stat. Softw. 4, i02 (1999)
Bell, C. D., Soltis, D. E. & Soltis, P. S. The age of the angiosperms: a molecular timescale without a clock. Evolution 59, 1245–1258 (2005)
Schneider, H. et al. Ferns diversified in the shadow of angiosperms. Nature 428, 553–557 (2004)
Article ADS CAS Google Scholar
Freeling, M. Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. Annu. Rev. Plant Biol. 60, 433–453 (2009)
Kassahn, K. S., Dang, V. T., Wilkins, S. J., Perkins, A. C. & Ragan, M. A. Evolution of gene function and regulatory control after whole-genome duplication: comparative analyses in vertebrates. Genome Res. 19, 1404–1418 (2009)
Devlin, P. F., Patel, S. R. & Whitelam, G. C. Phytochrome E influences internode elongation and flowering time in Arabidopsis . Plant Cell 10, 1479–1487 (1998)
Dechaine, J. M., Gardner, G. & Weinig, C. Phytochromes differentially regulate seed germination responses to light quality and temperature cues during seed maturation. Plant Cell Environ. 32, 1297–1309 (2009)
Mathews, S., Burleigh, J. G. & Donoghue, M. J. Adaptive evolution in the photosensory domain of phytochrome A in early angiosperms. Mol. Biol. Evol. 20, 1087–1097 (2003)
Parry, G. et al. Complex regulation of the TIR1/AFB family of auxin receptors. Proc. Natl Acad. Sci. USA 106, 22540–22545 (2009)
Article ADS CAS Google Scholar
Hu, W., dePamphilis, C. W. & Ma, H. Phylogenetic analysis of the plant-specific zinc finger-homeobox and mini zinc finger gene families. J. Integr. Plant Biol. 50, 1031–1045 (2008)
Prigge, M. J. & Clark, S. E. Evolution of the class III HD-Zip gene family in land plants. Evol. Dev. 8, 350–361 (2006)
Buggs, R. J. et al. Gene loss and silencing in Tragopogon miscellus (Asteraceae): comparison of natural and synthetic allotetraploids. Heredity 103, 73–81 (2009)
Vandepoele, K., Simillion, C. & Van de Peer, Y. Detecting the undetectable: uncovering duplicated segments in Arabidopsis by comparison with rice. Trends Genet. 18, 606–608 (2002)
Blanc, G. & Wolfe, K. H. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16, 1667–1678 (2004)
Van de Peer, Y., Fawcett, J. A., Proost, S., Sterck, L. & Vandepoele, K. The flowering world: a tale of duplications. Trends Plant Sci. 14, 680–688 (2009)
Li, L., Stoeckert, C. J., Jr & Roos, D. S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178–2189 (2003)
Proost, S. et al. PLAZA: a comparative genomics resource to study gene and genome evolution in plants. Plant Cell 21, 3718–3731 (2009)
Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004)
Capella-Gutierrez, S., Silla-Martinez, J. M. & Gabaldon, T. TrimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009)
Thompson, J. D., Gibson, T. J. & Higgins, D. G. Multiple sequence alignment using ClustalW and ClustalX. Curr. Protoc. Bioinf. 2.3.1–2.3.22. (2002)
Stamatakis, A., Ludwig, T. & Meier, H. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21, 456–463 (2005)
Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688–2690 (2006)
Felsenstein, J. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27, 401–410 (1978)
Hendy, M. D. & Penny, D. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38, 297–309 (1989)
Sanderson, M. J. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19, 301–302 (2003)
Rensing, S. A. et al. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319, 64–69 (2008)
Article ADS CAS Google Scholar
Kenrick, P. & Crane, P. R. The origin and early evolution of plants on land. Nature 389, 33–39 (1997)
Article ADS CAS Google Scholar
Miller, C. N. J. Implications of fossil conifers for the phylogenetic relationships of living families. Bot. Rev. 65, 239–277 (1999)
Doyle, J. A. & Hotton, C. L. in Pollen and Spores: Patterns of Diversification (eds Blackmore, S. & Barnes, S. H. ) 169–195 (Clarendon, 1991)
Suyama, M., Torrents, D. & Bork, P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 34, W609–W612 (2006)
Goldman, N. & Yang, Z. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11, 725–736 (1994)
CAS PubMed Google Scholar
Yang, Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555–556 (1997)
CAS Google Scholar
Ashburner, M. et al. Gene ontology: tool for the unification of biology. Nature Genet. 25, 25–29 (2000)
Zdobnov, E. M. & Apweiler, R. InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17, 847–848 (2001)
Du, Z., Zhou, X., Ling, Y., Zhang, Z. & Su, Z. agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 38, W64–W70 (2010)