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Nat Genet. 2015 Dec;47(12):1435-42. doi: 10.1038/ng.3435. Epub 2015 Nov 2.

The pineapple genome and the evolution of CAM photosynthesis.

Author information

1
Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.
2
Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.
3
Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
4
Donald Danforth Plant Science Center, St. Louis, Missouri, USA.
5
iPlant Collaborative/University of Arizona, Tucson, Arizona, USA.
6
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
7
Department of Plant Biology, University of Georgia, Athens, Georgia, USA.
8
Hawaii Agriculture Research Center, Kunia, Hawaii, USA.
9
Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, Hawaii, USA.
10
Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada, USA.
11
Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada.
12
Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.
13
Institut de Recherche pour le Développement, Diversité Adaptation et Développement des Plantes, Montpellier, France.
14
Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA.
15
Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Gesellschaft Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
16
Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, Texas, USA.
17
Department of Biological Sciences, Youngstown State University, Youngstown, Ohio, USA.
18
Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.
19
Australian Research Council (ARC) Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus Urrbrae, Adelaide, South Australia, Australia.
20
Department of Agronomy, National Taiwan University, Taipei, Taiwan.
21
W.M. Keck Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
22
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
23
US Department of Agriculture-Agricultural Research Service (USDA-ARS), Pacific Basin Agricultural Research Center, Hilo, Hawaii, USA.
24
Department of Biochemistry and Molecular Biology, Noble Research Center, Oklahoma State University, Stillwater, Oklahoma, USA.
25
Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, USA.
26
Department of Plant Sciences, University of Oxford, Oxford, UK.

Abstract

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 ρ 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.

PMID:
26523774
PMCID:
PMC4867222
DOI:
10.1038/ng.3435
[Indexed for MEDLINE]
Free PMC Article

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