The pineapple genome and the evolution of CAM photosynthesis
Ray Ming
(1, 2)
,
Robert Vanburen
(1, 2)
,
Ching Man Wai
(1, 2)
,
Haibao Tang
(1, 2, 3)
,
Michael C. Schatz
(4)
,
John E. Bowers
(5)
,
Eric Lyons
(3)
,
Ming-Li Wang
,
Jung Chen
(6)
,
Eric Biggers
(4)
,
Jisen Zhang
(2, 1)
,
Lixian Huang
(2, 1)
,
Lingmao Zhang
(1, 2)
,
Wenjing Miao
(1, 2)
,
Jian Zhang
(1, 2)
,
Zhangyao Ye
(1, 2)
,
Chenyong Miao
(1, 2)
,
Zhicong Lin
(1, 2)
,
Hao Wang
(5)
,
Hongye Zhou
(5)
,
Won C. Yim
(7)
,
Henry D. Priest
,
Chunfang Zheng
(8)
,
Margaret Woodhouse
(9)
,
Patrick P. Edger
(9)
,
Romain Guyot
(10, 11)
,
Hao-Bo Guo
(12)
,
Hong Guo
(12)
,
Guangyong Zheng
,
Ratnesh Singh
(13)
,
Anupma Sharma
(13)
,
Xiangjia Min
(14)
,
Yun Zheng
(15)
,
Hayan Lee
(4)
,
James Gurtowski
(4)
,
Fritz J. Sedlazeck
(4)
,
Alex Harkess
(5)
,
Michael R Mckain
,
Zhenyang Liao
(2, 1)
,
Jingping Fang
(1, 2)
,
Juan Liu
(2, 1)
,
Xiaodan Zhang
(1, 2)
,
Qing Zhang
(1, 2)
,
Weichang Hu
(1, 2)
,
Yuan Qin
(1, 2)
,
Kai Wang
(1, 2)
,
Li-Yu Chen
(2, 1)
,
Neil Shirley
(16)
,
Yann-Rong Lin
(17)
,
Li-Yu Liu
(17)
,
Alvaro G. Hernandez
(1)
,
Chris L. Wright
(1)
,
Vincent Bulone
(16)
,
Gerald A. Tuskan
(18)
,
Katy Heath
(1)
,
Francis Zee
,
Paul H. Moore
,
Ramanjulu Sunkar
(19)
,
James H. Leebens-Mack
(5)
,
Todd Mockler
,
Jeffrey L Bennetzen
(5)
,
Michael Freeling
(9)
,
David Sankoff
(8)
,
Andrew H. Paterson
(5)
,
Xinguang Zhu
(18)
,
Xiaohan Yang
(18)
,
J Andrew C Smith
(20)
,
John C. Cushman
(7)
,
Robert E. Paull
(6)
,
Qingyi Yu
(13)
1
UIUC -
University of Illinois at Urbana-Champaign [Urbana]
2 FAFU - Fujian Agriculture and Forestry University
3 University of Arizona
4 CSHL - Cold Spring Harbor Laboratory
5 University of Georgia [USA]
6 University of Hawaii
7 University of Nevada [Reno]
8 University of Ottawa [Ottawa]
9 UC Berkeley - University of California [Berkeley]
10 UMR IPME - UMR - Interactions Plantes Microorganismes Environnement
11 UMR DIADE - Diversité, adaptation, développement des plantes
12 The University of Tennessee [Knoxville]
13 Texas A&M University System
14 YSU - Youngstown State University
15 KMUST - Kunming University of Science and Technology
16 University of South Australia [Adelaide]
17 NTU - National Taiwan University [Taiwan]
18 ORNL - Oak Ridge National Laboratory [Oak Ridge]
19 OU - University of Oklahoma
20 University of Oxford
2 FAFU - Fujian Agriculture and Forestry University
3 University of Arizona
4 CSHL - Cold Spring Harbor Laboratory
5 University of Georgia [USA]
6 University of Hawaii
7 University of Nevada [Reno]
8 University of Ottawa [Ottawa]
9 UC Berkeley - University of California [Berkeley]
10 UMR IPME - UMR - Interactions Plantes Microorganismes Environnement
11 UMR DIADE - Diversité, adaptation, développement des plantes
12 The University of Tennessee [Knoxville]
13 Texas A&M University System
14 YSU - Youngstown State University
15 KMUST - Kunming University of Science and Technology
16 University of South Australia [Adelaide]
17 NTU - National Taiwan University [Taiwan]
18 ORNL - Oak Ridge National Laboratory [Oak Ridge]
19 OU - University of Oklahoma
20 University of Oxford
Haibao Tang
- Fonction : Auteur
- PersonId : 775056
- ORCID : 0000-0002-3460-8570
Ming-Li Wang
- Fonction : Auteur
Hao Wang
- Fonction : Auteur
- PersonId : 762829
- ORCID : 0000-0002-9819-7483
- IdRef : 177547057
Henry D. Priest
- Fonction : Auteur
Romain Guyot
- Fonction : Auteur
- PersonId : 801032
- IdHAL : romain-guyot
- ORCID : 0000-0002-7016-7485
- IdRef : 224213946
Guangyong Zheng
- Fonction : Auteur
Ratnesh Singh
- Fonction : Auteur
- PersonId : 818197
- ORCID : 0000-0001-5647-3390
Michael R Mckain
- Fonction : Auteur
Qing Zhang
- Fonction : Auteur
- PersonId : 770376
- ORCID : 0000-0002-6595-8995
Kai Wang
- Fonction : Auteur
- PersonId : 763158
- ORCID : 0000-0001-6269-3517
Francis Zee
- Fonction : Auteur
Paul H. Moore
- Fonction : Auteur
Todd Mockler
- Fonction : Auteur
- PersonId : 801135
- ORCID : 0000-0002-0462-5775
J Andrew C Smith
- Fonction : Auteur
- PersonId : 818198
- ORCID : 0000-0001-9188-0258
Résumé
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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