An example of the power of genome study: floral MADS-box genes in the Amborella genome Sangtae Kim Department of Biology, Sungshin University Amborella genome has published Dec. 20, 2013 The Amborella Genome and the Evolution of Flowering Plants Amborella Genome Project‡ ‡All authors with affiliations and contributions are listed at the end of the paper. Amborella Genome Project Authorship of this paper should be cited as “Amborella Genome Project.” Participants are arranged by working group, and then are listed in alphabetical order. Significant contributions (†) and the author for correspondence (*) are indicated within each working group. Joshua P. Der (project manager), Srikar Chamala, Andre S. Chanderbali, and James C. Estill made significant and equal contributions to this work. Research leadership: Victor A. Albert1, W. Bradley Barbazuk2, Claude W. dePamphilis3,4,* ([email protected]), Joshua P. Der3,4,†, James Leebens-Mack5, Hong Ma3,4,6, Steve Rounsley7,8, David Sankoff9, Stephan Schuster10, Douglas E. Soltis2,11, Pamela S. Soltis2,11, Susan R. Wessler12, Rod A. Wing7 Genome sequencing and assembly: Victor A. Albert1, W. Bradley Barbazuk2,* ([email protected]), Srikar Chamala2,†, Andre S. Chanderbali2, Claude W. dePamphilis3,4, Joshua P. Der3,4, Ronald Determann13, Raju Jetty7, James Leebens-Mack5, Hong Ma3,4,6, Paula Ralph3, Steve Rounsley7,8, Stephan Schuster10, Douglas E. Soltis2,11, Pamela S. Soltis2,11, Jason Talag7, Lynn Tomsho10, Brandon Walts2, Stefan Wanke14, Rod A. Wing7 Cytogenetics: Victor A. Albert1, W. Bradley Barbazuk2, Srikar Chamala2, Andre S. Chanderbali2,†, Tien-Hao Chang1, Ronald Determann13, Tianying Lan1, Douglas E. Soltis2,11,* ([email protected]), Pamela S. Soltis2,11 Genome annotation and database development: Siwaret Arikit15, Michael Axtell3,4, Saravanaraj Ayyampalayam5, W. Bradley Barbazuk2, James M. Burnette, III12, Srikar Chamala2, Emanuel De Paoli16, Claude W. dePamphilis3,4, Joshua P. Der3,4, James C. Estill5,†, Alex Harkess5, Yuannian Jiao3,17, James Leebens-Mack5,* ([email protected]), Kun Liu12, Wenbin Mei2, Blake Meyers15, Saima Shahid4, Eric Wafula3, Brandon Walts2, Susan R. Wessler12, Jixian Zhai15, Xiaoyu Zhang5 Synteny analysis: Victor A. Albert1* ([email protected]), Lorenzo Carretero-Paulet1, Claude W. dePamphilis3,4, Joshua P. Der3,4, Yuannian Jiao3,17, James Leebens-Mack5, Eric Lyons7,18, David Sankoff9,†, Haibao Tang19, Eric Wafula3, Chunfang Zheng9 Global gene family analysis: Victor A. Albert1, Naomi S. Altman20, W. Bradley Barbazuk2, Claude W. dePamphilis3,4,* ([email protected]), Joshua P. Der3,4,†, James C. Estill5, Yuannian Jiao3,17,†, James Leebens-Mack5, Kun Liu12, Wenbin Mei2, Eric Wafula3 Targeted gene family curation and analysis: Naomi S. Altman20, Siwaret Arikit15, Michael Axtell3,4, Srikar Chamala2, Andre S. Chanderbali2, Feng Chen21, Jian-Qun Chen22, Vincent Chiang23, Emanuel De Paoli16, Claude W. dePamphilis3,4, Joshua P. Der3,4,* ([email protected]), Ronald Determann13, Bruno Fogliani24, Chunce Guo25, Jesper Harholt26, Alex Harkess5, Claudette Job27, Dominique Job27, Sangtae Kim28, Hongzhi Kong25, James Leebens-Mack5, Guanglin Li21, Lin Li25, Jie Liu23, Hong Ma3,4,6, Blake Meyers15, Jongsun Park28, Xinshuai Qi2,29, Loïc Rajjou30, Valerie Sarramegna24, Ron Sederoff23, Saima Shahid4, Douglas E. Soltis2,11, Pamela S. Soltis2,11, Ying Hsuan Sun23, Peter Ulvskov26, Matthieu Villegente24, Jia-Yu Xue22, Ting-Feng Yeh31, Xianxian Yu25, Jixian Zhai15 Population genomics: Juan J. Acosta32, Victor A. Albert1, W. Bradley Barbazuk2, Riva A. Bruenn3, Alex de Kochko33, Claude W. dePamphilis3,4, Joshua P. Der3,4, Luis R. Herrera-Estrella34, Enrique Ibarr-Laclette34, Matias Kirst32, James Leebens-Mack5, Solon P. Pissis2, Valerie Poncet33, Stephan Schuster10, Douglas E. Soltis2,11, Pamela S. Soltis2,11,* ([email protected]), Lynn Tomsho10 (Amborella Genome Project, 2013. Science) 78 authors in 44 institutes from 12 countries In Science vol. 342 (Dec. 20, 2013) • The Amborella Genome and the Evolution of Flowering Plants (Amborella Genome Project, 2013) 11 pages of Research Article and 119 pages of Supplementary Materials • Related papers and reports in the same issue - Assembly and Validation of the Genome of the Nonmodel Basal Angiosperm Amborella (Chamala et al., 2013) Report - Horizontal Transfer of Entire Genomes via Mitochondrial Fusion in the Angiosperm Amborella (Rice et al., 2013) Research Article - Genomic Clues to the Ancestral Flowering Plants (Keith Adams, 2013) Perspective “News” in Nature New York Times Discovery News Sci-News Why Amborella? A sister to all other Angiosperms! … ? Darwin’s Abominable Mystery: explosive evolution and diversification of angiosperms - Charles Darwin letter to Joseph Dalton Hooker, 22 July 1879. “…the rapid rise and early diversification of angiosperms is an abominable mystery…” * ? Early branching angiosperm (sister to all other angiosperms): Ranalian complex? Amentiferae? Magnolia? Drimys? Ceratophyllum? Eudicots Core- Fagales Walnuts, chestnut Cucurbitales Squash eudicots Rosales Apples, strawberries Debates on the most-basal angiosperm Fabales Legumes Zygophyllales Creosote plant Celastrales 1) STRIGHT PHYLOGENETIC ANALYSIS Oxalidales Star fruit Malpighiales Passion fruit Sapindales Citrus, cashews Malvales Cotton, cocoa Brassicales Arabidopsis, mustard Crossosomatales Myrtales Pomegranate Gernaliales Saxifragales Gooseberry Lamiales Antirrhinum, olive Solanales Tomato, green pepper Gentianales Coffee Garryales Asterales Sunflower Dipsacales Elderberry Soltis et al. (1999) Nature Apiales Dill, fennel Aquifoliales Cornales Ericales Blueberry, cranberry Berberidopsidales - Selected 500 taxa Santalales Caryophyllales Buckwheat, quinoa - Multi-gene analyses: Gunnerales Buxales rbcL+atpB+18S Trochodendrales Proteales Macadamia nut Sabiaceae Ranunculales Poppy Monocots Ceratophyllales Chloranthales Magnoliales Nutmeg Laurales Avocado Piperales Black pepper Winterales Illiciaceae Star anise Schisandraceae Austrobaileyaceae Nymphaeaceae Amborellaceae Gymnosperms Debates on the most-basal angiosperm 2) TREE NETWORK OF DUPLICATED GENES AP3 subfamily STDEF.Solanum NTDEF.Nicotiana PI subfamily RfPI.1.Ranunculus SmAP3.Sagittaria EbAP3.1.Eupomatia MfPI.Michelia MfAP3.Michelia # # CUM26Cucumis * * * Kim et al. (2004) AJB Phylogeny of B-class MADS-box genes Debates on the most-basal angiosperm 3) Structure of B-class genes also supports that Amborella is a basal-most angiosperm Eudicots Core- Fagales Walnuts, chestnut Cucurbitales Squash eudicots •End of debates? Rosales Apples, strawberries Fabales Legumes Zygophyllales Creosote plant Soltis et al., 1999. Celastrales Oxalidales Star fruit Malpighiales Passion fruit Mathews and Donoghue, 1999 Sapindales Citrus, cashews Qiu et al., 1999 Malvales Cotton, cocoa Brassicales Arabidopsis, mustard Soltis, …, Kim, 2000 Crossosomatales Savolainen et al., 2000 Myrtales Pomegranate Gernaliales Barkman et al., 2000 Saxifragales Gooseberry Zanis et al., 2002 Lamiales Antirrhinum, olive Solanales Tomato, green pepper Kuzoff and Gasser, 2000 Gentianales Coffee Zanis et al., 2002 Garryales Asterales Sunflower Borsch et al., 2003 Dipsacales Elderberry Apiales Dill, fennel Goremykin et al., 2003 Aquifoliales Hilu et al., 2003 Cornales Ericales Blueberry, cranberry Soltis and Soltis, 2004 Berberidopsidales Soltis et al., 2004 Santalales Caryophyllales Buckwheat, quinoa Kim et al., 2004 Gunnerales Martin et al., 2005 Buxales Trochodendrales Leebens-Mack et al., 2005 Goremykin et al., Proteales Macadamia nut 2006 Sabiaceae Ranunculales Poppy Moore et al., 2007 Jansen et al., 2007 Soltis et al., 2012 Monocots … Ceratophyllales Chloranthales Magnoliales Nutmeg Laurales Avocado Piperales Black pepper Winterales Illiciaceae Star anise Schisandraceae Austrobaileyaceae Nymphaeaceae Amborellaceae Gymnosperms Amborella genome? Evolutionary reference of angiosperms Asterales Dipsacales Apiales Aquifoliales RECENT GENOME STUDIES Campanulids (Euasterids II) Garryales Asterids Gentianales ON ANGIOSPERM EVOLUTION Laminales Mimulus Solanales Solanum, Capsella Lamiids Ericales (Euasterids I) Cornales Sapindales Citrus Malvales Theobroma, Gossypium Brassicales Arabidopsis, Thellungiella, Carica, Brassica Malvids • Summary of angiosperm (Eurosids II) Fagales Cucurbitales Cucumis, Citrullus phylogeny based on recent Rosales Malus, Fragaria, Prunus, Pyrus, Cannabis Rosids Fabales Glycine, Medicago, Lotus, Cicer, Cajanus, Phaseolus molecular phylogenetic Zygophyllales Fabids Celestrales (Eurosid I) studies (Soltis et al., 2012; Oxalidales Malpighiales Populus, Ricinus, Manihot, Hevea, Linum Moore et al., 2007; Jansen Vitales Vitis Geraniales et al., 2007) Myrtales Eucalyptus Saxifragales Caryphyllales Beta Core- Santalales eudicots • Published or downloadable Beberidopsidales Gunnerales genome sequences on the Buxaceae Trochodendraceae Proteales Basal GenBank. Genomes of Sabiaceae eudicots EUDICOTS FOURTY angiosperm Aquilegia Ranunculales Euptelea genera have been Ceratophyllales Oryza Sorghum sequenced as of Dec. 2013. Zea Brachypodium MONOCOTS Phoenix Musa Acorus Setaria Canellales Basal Piperales Angiosperms Magnoliales Magnoliids Laurales Chloranthus Austrobailales Nymphaeaceae Hydatellaceae Amborella EXTENT GYMNOSPERMS Staminode Amborella trichopoda Tepals Carpel • Shrub, New Caledonia • Unisexual small flowers • Parts spirally arranged • Moderate number of parts • Undifferentiated perianth Carpel Tepals Staminode female Stamen Tepal male Amborella genome assembly and validation • Genome size: ~870Mb • Assembled over