The Amborella Genome and the Evolution of Flowering Plants

Victor A. Albert; W. Bradley Barbazuk; Claude W. dePamphilis; Joshua P. Der; James Leebens-Mack; Hong Ma; Jeffrey D. Palmer; Steve Rounsley; David Sankoff; Stephan C. Schuster; Douglas E. Soltis; Pamela S. Soltis; Susan R. Wessler; Rod A. Wing; Victor A. Albert; Jetty S. S. Ammiraju; W. Bradley Barbazuk; Srikar Chamala; Andre S. Chanderbali; Claude W. dePamphilis; Joshua P. Der; Ronald Determann; James Leebens-Mack; Hong Ma; Paula Ralph; Steve Rounsley; Stephan C. Schuster; Douglas E. Soltis; Pamela S. Soltis; Jason Talag; Lynn Tomsho; Brandon Walts; Stefan Wanke; Rod A. Wing; Victor A. Albert; W. Bradley Barbazuk; Srikar Chamala; Andre S. Chanderbali; Tien-Hao Chang; Ronald Determann; Tianying Lan; Douglas E. Soltis; Pamela S. Soltis; Siwaret Arikit; Michael J. Axtell; Saravanaraj Ayyampalayam; W. Bradley Barbazuk; James M. Burnette III; Srikar Chamala; Emanuele De Paoli; Claude W. dePamphilis; Joshua P. Der; James C. Estill; Nina P. Farrell; Alex Harkess; Yuannian Jiao; James Leebens-Mack; Kun Liu; Wenbin Mei; Blake C. Meyers; Saima Shahid; Eric Wafula; Brandon Walts; Susan R. Wessler; Jixian Zhai; Xiaoyu Zhang; Victor A. Albert; Lorenzo Carretero-Paulet; Claude W. dePamphilis; Joshua P. Der; Yuannian Jiao; James Leebens-Mack; Eric Lyons; David Sankoff; Haibao Tang; Eric Wafula; Chunfang Zheng; Victor A. Albert; Naomi S. Altman; W. Bradley Barbazuk; Lorenzo Carretero-Paulet; Claude W. dePamphilis; Joshua P. Der; James C. Estill; Yuannian Jiao; James Leebens-Mack; Kun Liu; Wenbin Mei; Eric Wafula; Naomi S. Altman; Siwaret Arikit; Michael J. Axtell; Srikar Chamala; Andre S. Chanderbali; Feng Chen; Jian-Qun Chen; Vincent Chiang; Emanuele De Paoli; Claude W. dePamphilis; Joshua P. Der; Ronald Determann; Bruno Fogliani; Chunce Guo; Jesper Harholt; Alex Harkess; Claudette Job; Dominique Job; Sangtae Kim; Hongzhi Kong; James Leebens-Mack; Guanglin Li; Lin Li; Jie Liu; Hong Ma; Blake C. Meyers; Jongsun Park; Xinshuai Qi; Loic Rajjou; Valerie Burtet-Sarramegna; Ron Sederoff; Saima Shahid; Douglas E. Soltis; Pamela S. Soltis; Ying-Hsuan Sun; Peter Ulvskov; Matthieu Villegente; Jia-Yu Xue; Ting-Feng Yeh; Xianxian Yu; Jixian Zhai; Juan J. Acosta; Victor A. Albert; W. Bradley Barbazuk; Riva A. Bruenn; Srikar Chamala; Alexandre de Kochko; Claude W. dePamphilis; Joshua P. Der; Luis R. Herrera-Estrella; Enrique Ibarra-Laclette; Matias Kirst; James Leebens-Mack; Solon P. Pissis; Valerie Poncet; Stephan C. Schuster; Douglas E. Soltis; Pamela S. Soltis; Lynn Tomsho; Amborella Genome Project

doi:10.1126/science.1241089

The Amborella Genome and the Evolution of Flowering Plants

Victor A. Albert, W. Bradley Barbazuk, Claude W. dePamphilis, Joshua P. Der, James Leebens-Mack, Hong Ma, Jeffrey D. Palmer, Steve Rounsley, David Sankoff, Stephan C. Schuster, Douglas E. Soltis, Pamela S. Soltis, Susan R. Wessler, Rod A. Wing, Victor A. Albert, Jetty S. S. Ammiraju, W. Bradley Barbazuk, Srikar Chamala, Andre S. Chanderbali, Claude W. dePamphilisJoshua P. Der, Ronald Determann, James Leebens-Mack, Hong Ma, Paula Ralph, Steve Rounsley, Stephan C. Schuster, Douglas E. Soltis, Pamela S. Soltis, Jason Talag, Lynn Tomsho, Brandon Walts, Stefan Wanke, Rod A. Wing, Victor A. Albert, W. Bradley Barbazuk, Srikar Chamala, Andre S. Chanderbali, Tien-Hao Chang, Ronald Determann, Tianying Lan, Douglas E. Soltis, Pamela S. Soltis, Siwaret Arikit, Michael J. Axtell, Saravanaraj Ayyampalayam, W. Bradley Barbazuk, James M. Burnette III, Srikar Chamala, Emanuele De Paoli, Claude W. dePamphilis, Joshua P. Der, James C. Estill, Nina P. Farrell, Alex Harkess, Yuannian Jiao, James Leebens-Mack, Kun Liu, Wenbin Mei, Blake C. Meyers, Saima Shahid, Eric Wafula, Brandon Walts, Susan R. Wessler, Jixian Zhai, Xiaoyu Zhang, Victor A. Albert, Lorenzo Carretero-Paulet, Claude W. dePamphilis, Joshua P. Der, Yuannian Jiao, James Leebens-Mack, Eric Lyons, David Sankoff, Haibao Tang, Eric Wafula, Chunfang Zheng, Victor A. Albert, Naomi S. Altman, W. Bradley Barbazuk, Lorenzo Carretero-Paulet, Claude W. dePamphilis, Joshua P. Der, James C. Estill, Yuannian Jiao, James Leebens-Mack, Kun Liu, Wenbin Mei, Eric Wafula, Naomi S. Altman, Siwaret Arikit, Michael J. Axtell, Srikar Chamala, Andre S. Chanderbali, Feng Chen, Jian-Qun Chen, Vincent Chiang, Emanuele De Paoli, Claude W. dePamphilis, Joshua P. Der, Ronald Determann, Bruno Fogliani, Chunce Guo, Jesper Harholt, Alex Harkess, Claudette Job, Dominique Job, Sangtae Kim, Hongzhi Kong, James Leebens-Mack, Guanglin Li, Lin Li, Jie Liu, Hong Ma, Blake C. Meyers, Jongsun Park, Xinshuai Qi, Loic Rajjou, Valerie Burtet-Sarramegna, Ron Sederoff, Saima Shahid, Douglas E. Soltis, Pamela S. Soltis, Ying-Hsuan Sun, Peter Ulvskov, Matthieu Villegente, Jia-Yu Xue, Ting-Feng Yeh, Xianxian Yu, Jixian Zhai, Juan J. Acosta, Victor A. Albert, W. Bradley Barbazuk, Riva A. Bruenn, Srikar Chamala, Alexandre de Kochko, Claude W. dePamphilis, Joshua P. Der, Luis R. Herrera-Estrella, Enrique Ibarra-Laclette, Matias Kirst, James Leebens-Mack, Solon P. Pissis, Valerie Poncet, Stephan C. Schuster, Douglas E. Soltis, Pamela S. Soltis, Lynn Tomsho, Amborella Genome Project

Section for Plant Glycobiology

445 Citations (Scopus)

Abstract

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.

Original language	English
Article number	1241089
Journal	Science
Volume	342
Issue number	6165
Number of pages	10
ISSN	0036-8075
DOIs	https://doi.org/10.1126/science.1241089
Publication status	Published - 20 Dec 2013

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10.1126/science.1241089

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Albert, V. A., Barbazuk, W. B., dePamphilis, C. W., Der, J. P., Leebens-Mack, J., Ma, H., Palmer, J. D., Rounsley, S., Sankoff, D., Schuster, S. C., Soltis, D. E., Soltis, P. S., Wessler, S. R., Wing, R. A., Albert, V. A., Ammiraju, J. S. S., Barbazuk, W. B., Chamala, S., Chanderbali, A. S., ... Project, A. G. (2013). The Amborella Genome and the Evolution of Flowering Plants. Science, 342(6165), [1241089]. https://doi.org/10.1126/science.1241089

Albert, VA, Barbazuk, WB, dePamphilis, CW, Der, JP, Leebens-Mack, J, Ma, H, Palmer, JD, Rounsley, S, Sankoff, D, Schuster, SC, Soltis, DE, Soltis, PS, Wessler, SR, Wing, RA, Albert, VA, Ammiraju, JSS, Barbazuk, WB, Chamala, S, Chanderbali, AS, dePamphilis, CW, Der, JP, Determann, R, Leebens-Mack, J, Ma, H, Ralph, P, Rounsley, S, Schuster, SC, Soltis, DE, Soltis, PS, Talag, J, Tomsho, L, Walts, B, Wanke, S, Wing, RA, Albert, VA, Barbazuk, WB, Chamala, S, Chanderbali, AS, Chang, T-H, Determann, R, Lan, T, Soltis, DE, Soltis, PS, Arikit, S, Axtell, MJ, Ayyampalayam, S, Barbazuk, WB, Burnette III, JM, Chamala, S, De Paoli, E, dePamphilis, CW, Der, JP, Estill, JC, Farrell, NP, Harkess, A, Jiao, Y, Leebens-Mack, J, Liu, K, Mei, W, Meyers, BC, Shahid, S, Wafula, E, Walts, B, Wessler, SR, Zhai, J, Zhang, X, Albert, VA, Carretero-Paulet, L, dePamphilis, CW, Der, JP, Jiao, Y, Leebens-Mack, J, Lyons, E, Sankoff, D, Tang, H, Wafula, E, Zheng, C, Albert, VA, Altman, NS, Barbazuk, WB, Carretero-Paulet, L, dePamphilis, CW, Der, JP, Estill, JC, Jiao, Y, Leebens-Mack, J, Liu, K, Mei, W, Wafula, E, Altman, NS, Arikit, S, Axtell, MJ, Chamala, S, Chanderbali, AS, Chen, F, Chen, J-Q, Chiang, V, De Paoli, E, dePamphilis, CW, Der, JP, Determann, R, Fogliani, B, Guo, C, Harholt, J, Harkess, A, Job, C, Job, D, Kim, S, Kong, H, Leebens-Mack, J, Li, G, Li, L, Liu, J, Ma, H, Meyers, BC, Park, J, Qi, X, Rajjou, L, Burtet-Sarramegna, V, Sederoff, R, Shahid, S, Soltis, DE, Soltis, PS, Sun, Y-H, Ulvskov, P, Villegente, M, Xue, J-Y, Yeh, T-F, Yu, X, Zhai, J, Acosta, JJ, Albert, VA, Barbazuk, WB, Bruenn, RA, Chamala, S, de Kochko, A, dePamphilis, CW, Der, JP, Herrera-Estrella, LR, Ibarra-Laclette, E, Kirst, M, Leebens-Mack, J, Pissis, SP, Poncet, V, Schuster, SC, Soltis, DE, Soltis, PS, Tomsho, L & Project, AG 2013, 'The Amborella Genome and the Evolution of Flowering Plants', Science, vol. 342, no. 6165, 1241089. https://doi.org/10.1126/science.1241089

@article{922594c3e5a94fc9a2038f012c2af86b,

title = "The Amborella Genome and the Evolution of Flowering Plants",

abstract = "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.",

author = "Albert, {Victor A.} and Barbazuk, {W. Bradley} and dePamphilis, {Claude W.} and Der, {Joshua P.} and James Leebens-Mack and Hong Ma and Palmer, {Jeffrey D.} and Steve Rounsley and David Sankoff and Schuster, {Stephan C.} and Soltis, {Douglas E.} and Soltis, {Pamela S.} and Wessler, {Susan R.} and Wing, {Rod A.} and Albert, {Victor A.} and Ammiraju, {Jetty S. S.} and Barbazuk, {W. Bradley} and Srikar Chamala and Chanderbali, {Andre S.} and dePamphilis, {Claude W.} and Der, {Joshua P.} and Ronald Determann and James Leebens-Mack and Hong Ma and Paula Ralph and Steve Rounsley and Schuster, {Stephan C.} and Soltis, {Douglas E.} and Soltis, {Pamela S.} and Jason Talag and Lynn Tomsho and Brandon Walts and Stefan Wanke and Wing, {Rod A.} and Albert, {Victor A.} and Barbazuk, {W. Bradley} and Srikar Chamala and Chanderbali, {Andre S.} and Tien-Hao Chang and Ronald Determann and Tianying Lan and Soltis, {Douglas E.} and Soltis, {Pamela S.} and Siwaret Arikit and Axtell, {Michael J.} and Saravanaraj Ayyampalayam and Barbazuk, {W. Bradley} and {Burnette III}, {James M.} and Srikar Chamala and {De Paoli}, Emanuele and dePamphilis, {Claude W.} and Der, {Joshua P.} and Estill, {James C.} and Farrell, {Nina P.} and Alex Harkess and Yuannian Jiao and James Leebens-Mack and Kun Liu and Wenbin Mei and Meyers, {Blake C.} and Saima Shahid and Eric Wafula and Brandon Walts and Wessler, {Susan R.} and Jixian Zhai and Xiaoyu Zhang and Albert, {Victor A.} and Lorenzo Carretero-Paulet and dePamphilis, {Claude W.} and Der, {Joshua P.} and Yuannian Jiao and James Leebens-Mack and Eric Lyons and David Sankoff and Haibao Tang and Eric Wafula and Chunfang Zheng and Albert, {Victor A.} and Altman, {Naomi S.} and Barbazuk, {W. Bradley} and Lorenzo Carretero-Paulet and dePamphilis, {Claude W.} and Der, {Joshua P.} and Estill, {James C.} and Yuannian Jiao and James Leebens-Mack and Kun Liu and Wenbin Mei and Eric Wafula and Altman, {Naomi S.} and Siwaret Arikit and Axtell, {Michael J.} and Srikar Chamala and Chanderbali, {Andre S.} and Feng Chen and Jian-Qun Chen and Vincent Chiang and {De Paoli}, Emanuele and dePamphilis, {Claude W.} and Der, {Joshua P.} and Ronald Determann and Bruno Fogliani and Chunce Guo and Jesper Harholt and Alex Harkess and Claudette Job and Dominique Job and Sangtae Kim and Hongzhi Kong and James Leebens-Mack and Guanglin Li and Lin Li and Jie Liu and Hong Ma and Meyers, {Blake C.} and Jongsun Park and Xinshuai Qi and Loic Rajjou and Valerie Burtet-Sarramegna and Ron Sederoff and Saima Shahid and Soltis, {Douglas E.} and Soltis, {Pamela S.} and Ying-Hsuan Sun and Peter Ulvskov and Matthieu Villegente and Jia-Yu Xue and Ting-Feng Yeh and Xianxian Yu and Jixian Zhai and Acosta, {Juan J.} and Albert, {Victor A.} and Barbazuk, {W. Bradley} and Bruenn, {Riva A.} and Srikar Chamala and {de Kochko}, Alexandre and dePamphilis, {Claude W.} and Der, {Joshua P.} and Herrera-Estrella, {Luis R.} and Enrique Ibarra-Laclette and Matias Kirst and James Leebens-Mack and Pissis, {Solon P.} and Valerie Poncet and Schuster, {Stephan C.} and Soltis, {Douglas E.} and Soltis, {Pamela S.} and Lynn Tomsho and Project, {Amborella Genome}",

year = "2013",

month = dec,

day = "20",

doi = "10.1126/science.1241089",

language = "English",

volume = "342",

journal = "Science",

issn = "0036-8075",

publisher = "American Association for the Advancement of Science",

number = "6165",

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TY - JOUR

T1 - The Amborella Genome and the Evolution of Flowering Plants

AU - Albert, Victor A.

AU - Barbazuk, W. Bradley

AU - dePamphilis, Claude W.

AU - Der, Joshua P.

AU - Leebens-Mack, James

AU - Ma, Hong

AU - Palmer, Jeffrey D.

AU - Rounsley, Steve

AU - Sankoff, David

AU - Schuster, Stephan C.

AU - Soltis, Douglas E.

AU - Soltis, Pamela S.

AU - Wessler, Susan R.

AU - Wing, Rod A.

AU - Albert, Victor A.

AU - Ammiraju, Jetty S. S.

AU - Barbazuk, W. Bradley

AU - Chamala, Srikar

AU - Chanderbali, Andre S.

AU - dePamphilis, Claude W.

AU - Der, Joshua P.

AU - Determann, Ronald

AU - Leebens-Mack, James

AU - Ma, Hong

AU - Ralph, Paula

AU - Rounsley, Steve

AU - Schuster, Stephan C.

AU - Soltis, Douglas E.

AU - Soltis, Pamela S.

AU - Talag, Jason

AU - Tomsho, Lynn

AU - Walts, Brandon

AU - Wanke, Stefan

AU - Wing, Rod A.

AU - Albert, Victor A.

AU - Barbazuk, W. Bradley

AU - Chamala, Srikar

AU - Chanderbali, Andre S.

AU - Chang, Tien-Hao

AU - Determann, Ronald

AU - Lan, Tianying

AU - Soltis, Douglas E.

AU - Soltis, Pamela S.

AU - Arikit, Siwaret

AU - Axtell, Michael J.

AU - Ayyampalayam, Saravanaraj

AU - Barbazuk, W. Bradley

AU - Burnette III, James M.

AU - Chamala, Srikar

AU - De Paoli, Emanuele

AU - dePamphilis, Claude W.

AU - Der, Joshua P.

AU - Estill, James C.

AU - Farrell, Nina P.

AU - Harkess, Alex

AU - Jiao, Yuannian

AU - Leebens-Mack, James

AU - Liu, Kun

AU - Mei, Wenbin

AU - Meyers, Blake C.

AU - Shahid, Saima

AU - Wafula, Eric

AU - Walts, Brandon

AU - Wessler, Susan R.

AU - Zhai, Jixian

AU - Zhang, Xiaoyu

AU - Albert, Victor A.

AU - Carretero-Paulet, Lorenzo

AU - dePamphilis, Claude W.

AU - Der, Joshua P.

AU - Jiao, Yuannian

AU - Leebens-Mack, James

AU - Lyons, Eric

AU - Sankoff, David

AU - Tang, Haibao

AU - Wafula, Eric

AU - Zheng, Chunfang

AU - Albert, Victor A.

AU - Altman, Naomi S.

AU - Barbazuk, W. Bradley

AU - Carretero-Paulet, Lorenzo

AU - dePamphilis, Claude W.

AU - Der, Joshua P.

AU - Estill, James C.

AU - Jiao, Yuannian

AU - Leebens-Mack, James

AU - Liu, Kun

AU - Mei, Wenbin

AU - Wafula, Eric

AU - Altman, Naomi S.

AU - Arikit, Siwaret

AU - Axtell, Michael J.

AU - Chamala, Srikar

AU - Chanderbali, Andre S.

AU - Chen, Feng

AU - Chen, Jian-Qun

AU - Chiang, Vincent

AU - De Paoli, Emanuele

AU - dePamphilis, Claude W.

AU - Der, Joshua P.

AU - Determann, Ronald

AU - Fogliani, Bruno

AU - Guo, Chunce

AU - Harholt, Jesper

AU - Harkess, Alex

AU - Job, Claudette

AU - Job, Dominique

AU - Kim, Sangtae

AU - Kong, Hongzhi

AU - Leebens-Mack, James

AU - Li, Guanglin

AU - Li, Lin

AU - Liu, Jie

AU - Ma, Hong

AU - Meyers, Blake C.

AU - Park, Jongsun

AU - Qi, Xinshuai

AU - Rajjou, Loic

AU - Burtet-Sarramegna, Valerie

AU - Sederoff, Ron

AU - Shahid, Saima

AU - Soltis, Douglas E.

AU - Soltis, Pamela S.

AU - Sun, Ying-Hsuan

AU - Ulvskov, Peter

AU - Villegente, Matthieu

AU - Xue, Jia-Yu

AU - Yeh, Ting-Feng

AU - Yu, Xianxian

AU - Zhai, Jixian

AU - Acosta, Juan J.

AU - Albert, Victor A.

AU - Barbazuk, W. Bradley

AU - Bruenn, Riva A.

AU - Chamala, Srikar

AU - de Kochko, Alexandre

AU - dePamphilis, Claude W.

AU - Der, Joshua P.

AU - Herrera-Estrella, Luis R.

AU - Ibarra-Laclette, Enrique

AU - Kirst, Matias

AU - Leebens-Mack, James

AU - Pissis, Solon P.

AU - Poncet, Valerie

AU - Schuster, Stephan C.

AU - Soltis, Douglas E.

AU - Soltis, Pamela S.

AU - Tomsho, Lynn

AU - Project, Amborella Genome

PY - 2013/12/20

Y1 - 2013/12/20

N2 - 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.

AB - 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.

U2 - 10.1126/science.1241089

DO - 10.1126/science.1241089

M3 - Journal article

C2 - 24357323

SN - 0036-8075

VL - 342

JO - Science

JF - Science

IS - 6165

M1 - 1241089

ER -