The pineapple genome and the evolution of CAM photosynthesis

Ray Ming; Robert Vanburen; Ching Man Wai; Haibao Tang; Michael C. Schatz; John E. Bowers; Eric Lyons; Ming-Li Wang; Jung Chen; Eric Biggers; Jisen Zhang; Lixian Huang; Lingmao Zhang; Wenjing Miao; Jian Zhang; Zhangyao Ye; Chenyong Miao; Zhicong Lin; Hao Wang; Hongye Zhou; Won C. Yim; Henry D. Priest; Chunfang Zheng; Margaret Woodhouse; Patrick P. Edger; Romain Guyot; Hao-Bo Guo; Hong Guo; Guangyong Zheng; Ratnesh Singh; Anupma Sharma; Xiangjia Min; Yun Zheng; Hayan Lee; James Gurtowski; Fritz J. Sedlazeck; Alex Harkess; Michael R Mckain; Zhenyang Liao; Jingping Fang; Juan Liu; Xiaodan Zhang; Qing Zhang; Weichang Hu; Yuan Qin; Kai Wang; Li-Yu Chen; Neil Shirley; Yann-Rong Lin; Li-Yu Liu; Alvaro G. Hernandez; Chris L. Wright; Vincent Bulone; Gerald A. Tuskan; Katy Heath; Francis Zee; Paul H. Moore; Ramanjulu Sunkar; James H. Leebens-Mack; Todd Mockler; Jeffrey L Bennetzen; Michael Freeling; David Sankoff; Andrew H. Paterson; Xinguang Zhu; Xiaohan Yang; J Andrew C Smith; John C. Cushman; Robert E. Paull; Qingyi Yu

doi:10.1038/ng.3435

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The pineapple genome and the evolution of CAM photosynthesis

Journal article

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Peer reviewed

The pineapple genome and the evolution of CAM photosynthesis

Ray Ming, Robert Vanburen, Ching Man Wai, Haibao Tang, Michael C. Schatz, John E. Bowers, Eric Lyons, Ming-Li Wang, Jung Chen, Eric Biggers, …

Nature Genetics, Vol.47(12), pp.1435-1442

12/2015

DOI: https://doi.org/10.1038/ng.3435

PMCID: PMC4867222

PMID: 26523774

Abstract

DNA sequencing

Genomics

Plant genetics

Pineapple (Ananas comosus (L.) Merr.) is the most economically valuable crop possessing crassulacean acid metabolism (CAM), a photosynthetic carbon assimilation pathway with high water-use efficiency, and the second most important tropical fruit. We sequenced the genomes of pineapple varieties F153 and MD2 and a wild pineapple relative, Ananas bracteatus accession CB5. The pineapple genome has one fewer ancient whole-genome duplication event than sequenced grass genomes and a conserved karyotype with seven chromosomes from before the duplication event. The pineapple lineage has transitioned from C3 photosynthesis to CAM, with CAM-related genes exhibiting a diel expression pattern in photosynthetic tissues. CAM pathway genes were enriched with cis-regulatory elements associated with the regulation of circadian clock genes, providing the first cis-regulatory link between CAM and circadian clock regulation. Pineapple CAM photosynthesis evolved by the reconfiguration of pathways in C3 plants, through the regulatory neofunctionalization of preexisting genes and not through the acquisition of neofunctionalized genes via whole-genome or tandem gene duplication

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Title: The pineapple genome and the evolution of CAM photosynthesis
Creators - without role: Ray Ming - Fujian Agriculture and Forestry University
Robert Vanburen - University of Illinois Urbana-Champaign
Ching Man Wai - Fujian Agriculture and Forestry University
Haibao Tang - Fujian Agriculture and Forestry University
Michael C. Schatz - Cold Spring Harbor Laboratory
John E. Bowers - University of Georgia
Eric Lyons - University of Arizona
Ming-Li Wang - Hawaii Agriculture Research Center
Jung Chen - University of Hawaii System
Eric Biggers - Cold Spring Harbor Laboratory
Jisen Zhang - Fujian Agriculture and Forestry University
Lixian Huang - Fujian Agriculture and Forestry University
Lingmao Zhang - Fujian Agriculture and Forestry University
Wenjing Miao - Fujian Agriculture and Forestry University
Jian Zhang - Fujian Agriculture and Forestry University
Zhangyao Ye - Fujian Agriculture and Forestry University
Chenyong Miao - Fujian Agriculture and Forestry University
Zhicong Lin - University of Illinois Urbana-Champaign
Hao Wang - University of Georgia
Hongye Zhou - University of Georgia
Won C. Yim - University of Nevada, Reno
Henry D. Priest - Donald Danforth Plant Science Center
Chunfang Zheng - University of Ottawa
Margaret Woodhouse - University of California, Berkeley
Patrick P. Edger - University of California, Berkeley
Romain Guyot - Université de Montpellier, Plant Health Institute of Montpellier - PHIM
Hao-Bo Guo - University of Tennessee at Knoxville
Hong Guo - University of Tennessee at Knoxville
Guangyong Zheng - Shanghai Institutes for Biological Sciences
Ratnesh Singh - Texas A&M University System
Anupma Sharma - Texas A&M University System
Xiangjia Min - Youngstown State University
Yun Zheng - Kunming University of Science and Technology
Hayan Lee - Cold Spring Harbor Laboratory
James Gurtowski - Cold Spring Harbor Laboratory
Fritz J. Sedlazeck - Cold Spring Harbor Laboratory
Alex Harkess - University of Georgia
Michael R Mckain - Donald Danforth Plant Science Center
Zhenyang Liao - Fujian Agriculture and Forestry University
Jingping Fang - Fujian Agriculture and Forestry University
Juan Liu - Fujian Agriculture and Forestry University
Xiaodan Zhang - Fujian Agriculture and Forestry University
Qing Zhang - Fujian Agriculture and Forestry University
Weichang Hu - Fujian Agriculture and Forestry University
Yuan Qin - Fujian Agriculture and Forestry University
Kai Wang - Fujian Agriculture and Forestry University
Li-Yu Chen - Fujian Agriculture and Forestry University
Neil Shirley - Australian Research Council
Yann-Rong Lin - National Taiwan University
Li-Yu Liu - National Taiwan University
Alvaro G. Hernandez - University of Illinois Urbana-Champaign
Chris L. Wright - University of Illinois Urbana-Champaign
Vincent Bulone - University of Adelaide
Gerald A. Tuskan - Oak Ridge National Laboratory
Katy Heath - University of Illinois Urbana-Champaign
Francis Zee - Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center
Paul H. Moore - Hawaii Agriculture Research Center
Ramanjulu Sunkar - Oklahoma State University
James H. Leebens-Mack - University of Georgia [USA]
Todd Mockler - Donald Danforth Plant Science Center
Jeffrey L Bennetzen - University of Georgia
Michael Freeling - University of California, Berkeley
David Sankoff - University of Ottawa
Andrew H. Paterson - University of Georgia
Xinguang Zhu - Oak Ridge National Laboratory
Xiaohan Yang - Oak Ridge National Laboratory
J Andrew C Smith - University of Oxford
John C. Cushman - University of Nevada, Reno
Robert E. Paull - University of Hawaii System
Qingyi Yu - Texas A&M University System
Publication Details: Nature Genetics, Vol.47(12), pp.1435-1442
Identifiers: 9936496009311
Academic Unit: Diversité, Adaptation et Développement des plantes - DIADE; Plant Health Institute of Montpellier - PHIM
Language: English
Resource Type: Journal article
Local Fields: hal-03478898