The Amborella Genome and the Evolution of Flowering Plants

被引：602

作者：

Albert, Victor A.

Barbazuk, W. Bradley ^{[2
,3
]}

dePamphilis, Claude W. ^{[4
,5
,6
,7
]}

Der, Joshua P. ^{[4
]}

Leebens-Mack, James ^{[8
]}

Ma, Hong ^{[4
,5
,9
,10
]}

Palmer, Jeffrey D. ^{[11
]}

Rounsley, Steve ^{[12
,13
,14
]}

Sankoff, David ^{[15
]}

Schuster, Stephan C. ^{[7
,16
,17
]}

Soltis, Douglas E. ^{[2
,3
,18
]}

Soltis, Pamela S. ^{[3
,18
]}

Wessler, Susan R. ^{[19
]}

Wing, Rod A. ^{[12
,13
,20
]}

Albert, Victor A.

Ammiraju, Jetty S. S. ^{[12
,13
,20
]}

Barbazuk, W. Bradley ^{[2
,3
]}

Chamala, Srikar ^{[2
]}

Chanderbali, Andre S. ^{[2
]}

dePamphilis, Claude W. ^{[4
,5
,6
,7
]}

Der, Joshua P. ^{[4
]}

Determann, Ronald ^{[21
]}

Leebens-Mack, James ^{[8
]}

Ma, Hong ^{[4
,5
,9
,10
]}

Ralph, Paula ^{[4
,5
]}

Rounsley, Steve ^{[12
,13
,14
]}

Schuster, Stephan C. ^{[7
,16
,17
]}

Soltis, Douglas E. ^{[2
,3
,18
]}

Soltis, Pamela S. ^{[3
,18
]}

Talag, Jason ^{[12
,13
,20
]}

Tomsho, Lynn ^{[16
]}

Walts, Brandon ^{[2
]}

Wanke, Stefan ^{[22
]}

Wing, Rod A. ^{[12
,13
,20
]}

Albert, Victor A.

Barbazuk, W. Bradley ^{[2
,3
]}

Chamala, Srikar ^{[2
]}

Chanderbali, Andre S. ^{[2
]}

Chang, Tien-Hao ^{[1
]}

Determann, Ronald ^{[21
]}

Lan, Tianying ^{[1
,23
]}

Soltis, Douglas E. ^{[2
,3
,18
]}

Soltis, Pamela S. ^{[3
,18
]}

Arikit, Siwaret ^{[24
]}

Axtell, Michael J. ^{[4
]}

Ayyampalayam, Saravanaraj ^{[8
]}

Barbazuk, W. Bradley ^{[2
,3
]}

Burnette, James M., III ^{[19
]}

Chamala, Srikar ^{[2
]}

De Paoli, Emanuele ^{[25
]}

机构：

[1] SUNY Buffalo, Dept Biol Sci, Buffalo, NY 14260 USA

[2] Univ Florida, Dept Biol, Gainesville, FL 32611 USA

[3] Univ Florida, Genet Inst, Gainesville, FL 32610 USA

[4] Penn State Univ, Dept Biol, University Pk, PA 16802 USA

[5] Penn State Univ, Huck Inst Life Sci, University Pk, PA 16802 USA

[6] Penn State Univ, Intercoll Plant Biol Grad Program, University Pk, PA 16802 USA

[7] Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA

[8] Univ Georgia, Dept Plant Biol, Athens, GA 30602 USA

[9] Fudan Univ, Sch Life Sci, State Key Lab Genet Engn, Shanghai 200433, Peoples R China

[10] Fudan Univ, Inst Genet, Inst Plant Biol, Ctr Evolutionary Biol,Inst Biomed Sci, Shanghai 200433, Peoples R China

[11] Indiana Univ, Dept Biol, Bloomington, IN 47405 USA

[12] Univ Arizona, Sch Biol Sci, Tucson, AZ 85721 USA

[13] Univ Arizona, Inst Collaborat Res BIO5, Tucson, AZ 85721 USA

[14] Dow AgroSci, Indianapolis, IN 46268 USA

[15] Univ Ottawa, Dept Math & Stat, Ottawa, ON K1N 6N5, Canada

[16] Penn State Univ, Dept Biochem & Mol Biol, University Pk, PA 16802 USA

[17] Singapore Ctr Environm Life Sci Engn, Singapore, Singapore

[18] Univ Florida, Florida Museum Nat Hist, Gainesville, FL 32611 USA

[19] Univ Calif Riverside, Dept Bot & Plant Sci, Riverside, CA 92521 USA

[20] Univ Arizona, Arizona Genom Inst, Tucson, AZ 85721 USA

[21] Atlanta Bot Garden, Atlanta, GA 30309 USA

[22] Tech Univ Dresden, Inst Bot, D-01062 Dresden, Germany

[23] Chongqing Univ Sci & Technol, Dept Biol, Chongqing 4000042, Peoples R China

[24] Univ Delaware, Delaware Biotechnol Inst, Newark, DE 19711 USA

[25] Univ Udine, Dipartimento Sci Agr & Ambientali, I-33100 Udine, Italy

[26] Univ Georgia, Plant Genome Mapping Lab, Athens, GA 30602 USA

[27] Univ Arizona, iPlant Collaborat, Tucson, AZ 85721 USA

[28] J Craig Venter Inst, Rockville, MD 20850 USA

[29] Penn State Univ, Dept Stat, University Pk, PA 16802 USA

[30] Univ Tennessee, Dept Plant Sci, Knoxville, TN 37996 USA

[31] Nanjing Univ, Sch Life Sci, Nanjing 210093, Jiangsu, Peoples R China

[32] N Carolina State Univ, Dept Forestry & Environm Resources, Raleigh, NC 27695 USA

[33] Univ New Caledonia, Lab Insulaire Vivant & Environm, Noumea 98851, New Caledonia

[34] Inst Agron Neo Caledonien IAC, Paita 98890, New Caledonia

[35] Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China

[36] Univ Copenhagen, Dept Plant & Environm Sci, DK-1871 Frederiksberg C, Denmark

[37] Univ Claude Bernard Lyon, Inst Natl Sci Appl Bayer CropSci Joint Lab UMR524, CNRS, Bayer CropSci, F-69263 Lyon 9, France

[38] Sungshin Womens Univ, Sch Biol Sci & Chem, Seoul 142732, South Korea

[39] Sungshin Womens Univ, Basic Sci Res Inst, Seoul 142732, South Korea

[40] Zhejiang Univ, Coll Life Sci, Key Lab Conservat Biol Endangered Wildlife, Minist Educ, Hangzhou 310058, Zhejiang, Peoples R China

[41] Zhejiang Univ, Coll Life Sci, Lab Systemat & Evolutionary Bot & Biodivers, Hangzhou 310058, Zhejiang, Peoples R China

[42] INRA AgroParisTech, Jean Pierre Bourgin Inst IJPB, UMR1318, Lab Excellence Saclay Plant Sci LabEx SPS, F-78026 Versailles, France

[43] Natl Chung Hsing Univ, Dept Forestry, Taichung 40227, Taiwan

[44] Natl Taiwan Univ, Sch Forestry & Resource Conservat, Taipei 10617, Taiwan

[45] Univ Florida, Sch Forest Resources & Conservat, Gainesville, FL 32611 USA

[46] Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA

[47] IRD, UMR Diversite Adaptat & Dev Plantes DIADE, F-34394 Montpellier 5, France

[48] Lab Nacl Genom Biodiversidad, Irapuato 36821, Mexico

[49] Heidelberg Inst Theoret Studies, Sci Comp Grp, D-69118 Heidelberg, Germany

来源：

SCIENCE | 2013年 / 342卷 / 6165期

基金：

美国国家科学基金会;

关键词：

BOX GENE FAMILY; WIDE ANALYSIS; PHYLOGENETIC ANALYSIS; EARLY DIVERSIFICATION; 11S GLOBULIN; ARABIDOPSIS; EXPRESSION; ANNOTATION; REGULATORS; SEQUENCE;

D O I：

10.1126/science.1241089

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Amborella trichopoda is strongly supported as the single living species of the sister lineage to all other extant flowering plants, providing a unique reference for inferring the genome content and structure of the most recent common ancestor (MRCA) of living angiosperms. Sequencing the Amborella genome, we identified an ancient genome duplication predating angiosperm diversification, without evidence of subsequent, lineage-specific genome duplications. Comparisons between Amborella and other angiosperms facilitated reconstruction of the ancestral angiosperm gene content and gene order in the MRCA of core eudicots. We identify new gene families, gene duplications, and floral protein-protein interactions that first appeared in the ancestral angiosperm. Transposable elements in Amborella are ancient and highly divergent, with no recent transposon radiations. Population genomic analysis across Amborella's native range in New Caledonia reveals a recent genetic bottleneck and geographic structure with conservation implications.

引用

页码：1467 / +

页数：11

共 87 条

[71] ANGIOSPERM PHYLOGENY: 17 GENES, 640 TAXA [J].

Soltis, Douglas E. ;

Smith, Stephen A. ;

Cellinese, Nico ;

Wurdack, Kenneth J. ;

Tank, David C. ;

Brockington, Samuel F. ;

Refulio-Rodriguez, Nancy F. ;

Walker, Jay B. ;

Moore, Michael J. ;

Carlsward, Barbara S. ;

Bell, Charles D. ;

Latvis, Maribeth ;

Crawley, Sunny ;

Black, Chelsea ;

Diouf, Diaga ;

Xi, Zhenxiang ;

Rushworth, Catherine A. ;

Gitzendanner, Matthew A. ;

Sytsma, Kenneth J. ;

Qiu, Yin-Long ;

Hilu, Khidir W. ;

Davis, Charles C. ;

Sanderson, Michael J. ;

Beaman, Reed S. ;

Olmstead, Richard G. ;

Judd, Walter S. ;

Donoghue, Michael J. ;

Soltis, Pamela S. .

AMERICAN JOURNAL OF BOTANY, 2011, 98 (04) :704-730

[72] POLYPLOIDY AND ANGIOSPERM DIVERSIFICATION [J].

Soltis, Douglas E. ;

Albert, Victor A. ;

Leebens-Mack, Jim ;

Bell, Charles D. ;

Paterson, Andrew H. ;

Zheng, Chunfang ;

Sankoff, David ;

dePamphilis, Claude W. ;

Wall, P. Kerr ;

Soltis, Pamela S. .

AMERICAN JOURNAL OF BOTANY, 2009, 96 (01) :336-348

[73] Gene body methylation is conserved between plant orthologs and is of evolutionary consequence [J].

Takuno, Shohei ;

Gaut, Brandon S. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2013, 110 (05) :1797-1802

[74] Conservation and divergence on plant seed 11S globulins based on crystal structures [J].

Tandang-Silvas, Mary Rose G. ;

Fukuda, Takako ;

Fukuda, Chisato ;

Prak, Krisna ;

Cabanos, Cerrone ;

Kimura, Aiko ;

Itoh, Takafumi ;

Mikami, Bunzo ;

Utsumi, Shigeru ;

Maruyama, Nobuyuki .

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 2010, 1804 (07) :1432-1442

[75] The population structure and floral biology of Amborella trichopoda (Amborellaceae) [J].

Thien, LB ;

Sage, TL ;

Jaffré, T ;

Bernhardt, P ;

Pontieri, V ;

Weston, PH ;

Malloch, D ;

Azuma, H ;

Graham, SW ;

McPherson, MA ;

Rai, HS ;

Sage, RF ;

Dupre, JL .

ANNALS OF THE MISSOURI BOTANICAL GARDEN, 2003, 90 (03) :466-490

[76]

Timell TE., 1965, Advances in Carbohydrate Chemistry, V20, P409, DOI DOI 10.1016/S0096-5332(08)60304-5

[77] A mystery unveiled [J].

Van de Peer, Yves .

GENOME BIOLOGY, 2011, 12 (05)

[78] The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution [J].

Verde, Ignazio ;

Abbott, Albert G. ;

Scalabrin, Simone ;

Jung, Sook ;

Shu, Shengqiang ;

Marroni, Fabio ;

Zhebentyayeva, Tatyana ;

Dettori, Maria Teresa ;

Grimwood, Jane ;

Cattonaro, Federica ;

Zuccolo, Andrea ;

Rossini, Laura ;

Jenkins, Jerry ;

Vendramin, Elisa ;

Meisel, Lee A. ;

Decroocq, Veronique ;

Sosinski, Bryon ;

Prochnik, Simon ;

Mitros, Therese ;

Policriti, Alberto ;

Cipriani, Guido ;

Dondini, Luca ;

Ficklin, Stephen ;

Goodstein, David M. ;

Xuan, Pengfei ;

Del Fabbro, Cristian ;

Aramini, Valeria ;

Copetti, Dario ;

Gonzalez, Susana ;

Horner, David S. ;

Falchi, Rachele ;

Lucas, Susan ;

Mica, Erica ;

Maldonado, Jonathan ;

Lazzari, Barbara ;

Bielenberg, Douglas ;

Pirona, Raul ;

Miculan, Mara ;

Barakat, Abdelali ;

Testolin, Raffaele ;

Stella, Alessandra ;

Tartarini, Stefano ;

Tonutti, Pietro ;

Arus, Pere ;

Orellana, Ariel ;

Wells, Christina ;

Main, Dorrie ;

Vizzotto, Giannina ;

Silva, Herman ;

Salamini, Francesco .

NATURE GENETICS, 2013, 45 (05) :487-494

[79] Genome-wide analysis of spatial gene expression in Arabidopsis flowers [J].

Wellmer, F ;

Riechmann, JL ;

Alves-Ferreira, M ;

Meyerowitz, EM .

PLANT CELL, 2004, 16 (05) :1314-1326

[80] Independent origins of syringyl lignin in vascular plants [J].

Weng, Jing-Ke ;

Li, Xu ;

Stout, Jake ;

Chapple, Clint .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (22) :7887-7892

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