The Amborella genome and the evolution of flowering plants

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

doi:10.1126/science.1241089

The Amborella genome and the evolution of flowering plants

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

Research output: Contribution to journal › Article › peer-review

655 Scopus citations

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 (US)
Journal	Science
Volume	342
Issue number	6165
DOIs	https://doi.org/10.1126/science.1241089
State	Published - Jan 1 2013
Externally published	Yes

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DePamphilis, C. W., Palmer, J. D., Rounsley, S., Sankoff, D., Schuster, S. C., Ammiraju, J. S. S., Barbazuk, W. B., Chamala, S., Chanderbali, A. S., Determann, R., Hong, M., Ralph, P., Talag, J., Tomsho, L., Walts, B., Wanke, S., Wing, R. A., Chang, T. H., Lan, T., ... Soltis, P. S. (2013). The Amborella genome and the evolution of flowering plants. Science, 342(6165). https://doi.org/10.1126/science.1241089

@article{8e989b425dbb42cbb47794dad4157691,

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

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doi = "10.1126/science.1241089",

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

TY - JOUR

T1 - The Amborella genome and the evolution of flowering plants

AU - DePamphilis, Claude W.

AU - Palmer, Jeffrey D.

AU - Rounsley, Steve

AU - Sankoff, David

AU - Schuster, Stephan C.

AU - Ammiraju, Jetty S.S.

AU - Barbazuk, W. Bradley

AU - Chamala, Srikar

AU - Chanderbali, Andre S.

AU - Determann, Ronald

AU - Hong, Ma

AU - Ralph, Paula

AU - Talag, Jason

AU - Tomsho, Lynn

AU - Walts, Brandon

AU - Wanke, Stefan

AU - Wing, Rod A.

AU - Chang, Tien Hao

AU - Lan, Tianying

AU - Soltis, Douglas E.

AU - Arikit, Siwaret

AU - Axtell, Michael J.

AU - Ayyampalayam, Saravanaraj

AU - Burnette, James M.

AU - De Paoli, Emanuele

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 - Wessler, Susan R.

AU - Zhai, Jixian

AU - Zhang, Xiaoyu

AU - Albert, Victor A.

AU - Carretero-Paulet, Lorenzo

AU - Lyons, Eric

AU - Tang, Haibao

AU - Zheng, Chunfang

AU - Altman, Naomi S.

AU - Chen, Feng

AU - Chen, Jian Qun

AU - Chiang, Vincent

AU - Der, Joshua P.

AU - Fogliani, Bruno

AU - Guo, Chunce

AU - Harholt, Jesper

AU - Job, Claudette

AU - Job, Dominique

AU - Kim, Sangtae

AU - Kong, Hongzhi

AU - Li, Guanglin

AU - Li, N.

AU - Liu, Jie

AU - Park, Jongsun

AU - Qi, Xinshuai

AU - Rajjou, Loïc

AU - Burtet-Sarramegna, Valérie

AU - Sederoff, Ron

AU - Sun, Ying Hsuan

AU - Ulvskov, Peter

AU - Villegente, Matthieu

AU - Xue, Jia Yu

AU - Yeh, Ting Feng

AU - Yu, Xianxian

AU - Acosta, Juan J.

AU - Bruenn, Riva A.

AU - De Kochko, Alexandre

AU - Herrera-Estrella, Luis R.

AU - Ibarra-Laclette, Enrique

AU - Kirst, Matias

AU - Pissis, Solon P.

AU - Poncet, Valérie

AU - Soltis, Pamela S.

N1 - Generated from Scopus record by KAUST IRTS on 2019-11-20

PY - 2013/1/1

Y1 - 2013/1/1

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.

UR - http://www.sciencemag.org/cgi/doi/10.1126/science.1241089

UR - http://www.scopus.com/inward/record.url?scp=84890829647&partnerID=8YFLogxK

U2 - 10.1126/science.1241089

DO - 10.1126/science.1241089

M3 - Article

SN - 1095-9203

VL - 342

JO - Science

JF - Science

IS - 6165

ER -

The Amborella genome and the evolution of flowering plants

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