title: The pineapple genome and the evolution of CAM photosynthesis.
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.
authors.affiliation: 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.|Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.|Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
authors.forename: Ray
authors.initials: R
authors.lastname: Ming
authors.affiliation: 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.|Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.|Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.|Donald Danforth Plant Science Center, St. Louis, Missouri, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: VanBuren
authors.affiliation: 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.|Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.|Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
authors.forename: Ching Man
authors.initials: CM
authors.lastname: Wai
authors.affiliation: 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.|Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.|iPlant Collaborative/University of Arizona, Tucson, Arizona, USA.
authors.forename: Haibao
authors.identifier: http://orcid.org/0000-0002-3460-8570
authors.initials: H
authors.lastname: Tang
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
authors.forename: Michael C
authors.initials: MC
authors.lastname: Schatz
authors.affiliation: Department of Plant Biology, University of Georgia, Athens, Georgia, USA.
authors.forename: John E
authors.initials: JE
authors.lastname: Bowers
authors.affiliation: iPlant Collaborative/University of Arizona, Tucson, Arizona, USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Lyons
authors.affiliation: Hawaii Agriculture Research Center, Kunia, Hawaii, USA.
authors.forename: Ming-Li
authors.initials: ML
authors.lastname: Wang
authors.affiliation: Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, Hawaii, USA.
authors.forename: Jung
authors.initials: J
authors.lastname: Chen
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Biggers
authors.affiliation: 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.|Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.
authors.forename: Jisen
authors.initials: J
authors.lastname: Zhang
authors.affiliation: 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.|Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.
authors.forename: Lixian
authors.initials: L
authors.lastname: Huang
authors.affiliation: 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.|Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.
authors.forename: Lingmao
authors.initials: L
authors.lastname: Zhang
authors.affiliation: 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.|Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.
authors.forename: Wenjing
authors.initials: W
authors.lastname: Miao
authors.affiliation: 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.|Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Zhang
authors.affiliation: 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.|Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.
authors.forename: Zhangyao
authors.initials: Z
authors.lastname: Ye
authors.affiliation: 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.|Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.
authors.forename: Chenyong
authors.initials: C
authors.lastname: Miao
authors.affiliation: 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.|Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.
authors.forename: Zhicong
authors.initials: Z
authors.lastname: Lin
authors.affiliation: Department of Plant Biology, University of Georgia, Athens, Georgia, USA.
authors.forename: Hao
authors.initials: H
authors.lastname: Wang
authors.affiliation: Department of Plant Biology, University of Georgia, Athens, Georgia, USA.
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authors.affiliation: Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada, USA.
authors.forename: Won C
authors.initials: WC
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authors.initials: HD
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authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.
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authors.initials: M
authors.lastname: Woodhouse
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.
authors.forename: Patrick P
authors.initials: PP
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authors.initials: R
authors.lastname: Guyot
authors.affiliation: Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA.
authors.forename: Hao-Bo
authors.initials: HB
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authors.affiliation: Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA.
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authors.initials: H
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authors.affiliation: 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.
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authors.forename: Ratnesh
authors.identifier: http://orcid.org/0000-0001-5647-3390
authors.initials: R
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authors.affiliation: Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, Texas, USA.
authors.forename: Anupma
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authors.affiliation: Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.
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authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
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authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
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authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
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authors.affiliation: 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.|Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.
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authors.affiliation: 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.|Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.
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authors.affiliation: 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.|Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.
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authors.affiliation: 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.|Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.
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authors.lastname: Qin
authors.affiliation: 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.|Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.
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authors.affiliation: 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.|Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.
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authors.affiliation: 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.
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authors.initials: N
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authors.affiliation: Department of Agronomy, National Taiwan University, Taipei, Taiwan.
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authors.affiliation: W.M. Keck Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
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authors.initials: CL
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authors.affiliation: 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.
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authors.initials: V
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authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
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authors.affiliation: Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
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authors.affiliation: US Department of Agriculture-Agricultural Research Service (USDA-ARS), Pacific Basin Agricultural Research Center, Hilo, Hawaii, USA.
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authors.initials: F
authors.lastname: Zee
authors.affiliation: Hawaii Agriculture Research Center, Kunia, Hawaii, USA.
authors.forename: Paul H
authors.initials: PH
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authors.affiliation: Department of Biochemistry and Molecular Biology, Noble Research Center, Oklahoma State University, Stillwater, Oklahoma, USA.
authors.forename: Ramanjulu
authors.initials: R
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authors.affiliation: Department of Plant Biology, University of Georgia, Athens, Georgia, USA.
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authors.initials: JH
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authors.identifier: http://orcid.org/0000-0002-0462-5775
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authors.affiliation: Department of Plant Biology, University of Georgia, Athens, Georgia, USA.
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authors.initials: JL
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authors.initials: M
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authors.affiliation: Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada.
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authors.lastname: Sankoff
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, USA.
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authors.initials: AH
authors.lastname: Paterson
authors.affiliation: 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.
authors.forename: Xinguang
authors.initials: X
authors.lastname: Zhu
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
authors.forename: Xiaohan
authors.initials: X
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authors.affiliation: Department of Plant Sciences, University of Oxford, Oxford, UK.
authors.forename: J Andrew C
authors.identifier: http://orcid.org/0000-0001-9188-0258
authors.initials: JA
authors.lastname: Smith
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada, USA.
authors.forename: John C
authors.initials: JC
authors.lastname: Cushman
authors.affiliation: Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, Hawaii, USA.
authors.forename: Robert E
authors.initials: RE
authors.lastname: Paull
authors.affiliation: Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, Texas, USA.
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authors.initials: Q
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mesh_terms: D031230:Ananas / Q000235:genetics*; D002874:Chromosome Mapping; D057890:Epigenomics; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D005819:Genetic Markers; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D010788:Photosynthesis / Q000502:physiology*
chemical_list: D005819:Genetic Markers