ArticleNature genetics2015
The pineapple genome and the evolution of CAM photosynthesis.
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Article in Nature genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 279 papers.
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279citing papers in PubMed
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279 citing papers in PubMed, 722 citations in OpenAlex.
- The heterozygous pineapple genome demonstrates the importance of haplotype-resolved plant genomes.Horticulture research · 2026Article
- Integrative analysis of CAM photosynthesis reveals its impact on primary metabolism in Yucca.Journal of experimental botany · 2026Article
- Nucleotide Combination Proportions Across Algae, Monocotyledons and Dicotyledons: Insights into Plant Genome Evolution.Plants (Basel, Switzerland) · 2026Article
- Adaptive Responses of Tropical Crops: A Multi-Scale Omics Integrated Perspective.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Physiology-Driven Irrigation Scheduling inPlants (Basel, Switzerland) · 2026Article
- Transposable element dynamics drive rapid evolution of centromere architecture in the Avena genus.Genome biology · 2026Article
- Toward telomere-to-telomere genomics in Fabaceae: Unlocking comparative and functional insights into symbiotic nitrogen fixation.Cell genomics · 2026Review
- Genome evolution through polyploidy: Enhancing plant stress resilience in agriculture.Proceedings of the National Academy of Sciences of the United States of America · 2026Review
- A PROMOTER::LUCIFERASE reporter system reveals key elements of the circadian regulation of Crassulacean acid metabolism (CAM) in Kalanchoë laxiflora Baker.The Plant journal : for cell and molecular biology · 2026Article
- Clusia genomes shed light on the evolution and diversity of crassulacean acid metabolism physiotypes.Nature communications · 2026Article
- Using reciprocally retained gene families to detect whole-genome multiplications in plants.Genome biology · 2026Article
- Divergent Transcriptional Architectures Beyond Core CAM Genes in Facultative and Constitutive CAM Species in Tillandsia L.Molecular ecology · 2026Article
- Two independent origins of XY sex chromosomes in Asparagus.Molecular biology and evolution · 2026Article
- Phylogenomics, ecomorphological evolution, and historical biogeography in Deuterocohnia (Bromeliaceae: Pitcairnioideae).American journal of botany · 2026Article
- Rhythmic Mechanisms Governing CAM Photosynthesis inInternational journal of molecular sciences · 2026Article
- Phylogenomic profile of exon-intron organization across angiosperms, their relationships with protein domains, and functional implications.Nature communications · 2026Article
- The function of the Arabidopsis receptor kinase THESEUS1 in plant cell wall integrity maintenance: from evolutionary origin to future perspectives.The Plant journal : for cell and molecular biology · 2026Review
- Chromosome-scale genome assembly, carbohydrate metabolism transcriptome atlas, and candidate genes for polysaccharide accumulation inFrontiers in plant science · 2026Article
- Cultivar-specific drought responses in pineapple revealed by concurrent changes in PSII and PSI energy partitioning.Frontiers in plant science · 2026Article
- Cryptic CAM photosynthesis in Joshua tree (Yucca brevifolia, Y. jaegeriana).The New phytologist · 2025Article
219 more citing papers are in PubMed but not listed here.
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Authors and funding
70 authors at 20 institutions in 7 countries.
Ray MingFujian 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.
Robert VanBurenFujian 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.
Ching Man WaiFujian 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.
Haibao TangFujian 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.ORCID http://orcid.org/0000-0002-3460-8570
Michael C SchatzCold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
John E BowersDepartment of Plant Biology, University of Georgia, Athens, Georgia, USA.
Eric LyonsiPlant Collaborative/University of Arizona, Tucson, Arizona, USA.
Ming-Li WangHawaii Agriculture Research Center, Kunia, Hawaii, USA.
Jung ChenDepartment of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, Hawaii, USA.
Eric BiggersCold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Jisen ZhangFujian 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.
Lixian HuangFujian 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.
Lingmao ZhangFujian 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.
Wenjing MiaoFujian 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.
Jian ZhangFujian 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.
Zhangyao YeFujian 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.
Chenyong MiaoFujian 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.
Zhicong LinFujian 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.
Hao WangDepartment of Plant Biology, University of Georgia, Athens, Georgia, USA.
Hongye ZhouDepartment of Plant Biology, University of Georgia, Athens, Georgia, USA.
Won C YimDepartment of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada, USA.
Henry D PriestDonald Danforth Plant Science Center, St. Louis, Missouri, USA.
Chunfang ZhengDepartment of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada.
Margaret WoodhouseDepartment of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.
Patrick P EdgerDepartment of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.
Romain GuyotInstitut de Recherche pour le Développement, Diversité Adaptation et Développement des Plantes, Montpellier, France.
Hao-Bo GuoDepartment of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA.
Hong GuoDepartment of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA.
Guangyong ZhengKey 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.
Ratnesh SinghTexas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, Texas, USA.ORCID http://orcid.org/0000-0001-5647-3390
Anupma SharmaTexas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, Texas, USA.
Xiangjia MinDepartment of Biological Sciences, Youngstown State University, Youngstown, Ohio, USA.
Yun ZhengFaculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.
Hayan LeeCold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
James GurtowskiCold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Fritz J SedlazeckCold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Alex HarkessDepartment of Plant Biology, University of Georgia, Athens, Georgia, USA.
Michael R McKainDonald Danforth Plant Science Center, St. Louis, Missouri, USA.
Zhenyang LiaoFujian 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.
Jingping FangFujian 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.
Juan LiuFujian 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.
Xiaodan ZhangFujian 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.
Qing ZhangFujian 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.
Weichang HuFujian 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.
Yuan QinFujian 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.
Kai WangFujian 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.
Li-Yu ChenFujian 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.
Neil ShirleyAustralian 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.
Yann-Rong LinDepartment of Agronomy, National Taiwan University, Taipei, Taiwan.
Li-Yu LiuDepartment of Agronomy, National Taiwan University, Taipei, Taiwan.
Alvaro G HernandezW.M. Keck Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
Chris L WrightW.M. Keck Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
Vincent BuloneAustralian 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.
Gerald A TuskanBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Katy HeathDepartment of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
Francis ZeeUS Department of Agriculture-Agricultural Research Service (USDA-ARS), Pacific Basin Agricultural Research Center, Hilo, Hawaii, USA.
Paul H MooreHawaii Agriculture Research Center, Kunia, Hawaii, USA.
Ramanjulu SunkarDepartment of Biochemistry and Molecular Biology, Noble Research Center, Oklahoma State University, Stillwater, Oklahoma, USA.
James H Leebens-MackDepartment of Plant Biology, University of Georgia, Athens, Georgia, USA.
Todd MocklerDonald Danforth Plant Science Center, St. Louis, Missouri, USA.ORCID http://orcid.org/0000-0002-0462-5775
Jeffrey L BennetzenDepartment of Plant Biology, University of Georgia, Athens, Georgia, USA.
Michael FreelingDepartment of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.
David SankoffDepartment of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada.
Andrew H PatersonPlant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, USA.
Xinguang ZhuKey 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.
Xiaohan YangBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
J Andrew C SmithDepartment of Plant Sciences, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0001-9188-0258
John C CushmanDepartment of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada, USA.
Robert E PaullDepartment of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, Hawaii, USA.
Qingyi YuTexas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, Texas, USA.
University of Illinois Urbana-Champaign · USFujian Agriculture and Forestry University · CNUniversity of Georgia · USCold Spring Harbor Laboratory · USDonald Danforth Plant Science Center · USTexas A&M University System · USUniversity of California, Berkeley · USAustralian Research Council · AUChinese Academy of Sciences · CNHawaii Agriculture Research Center · USNational Taiwan University · TWOak Ridge National Laboratory · USUniversity of Arizona · USUniversity of Hawaii System · USUniversity of Nevada, Reno · USUniversity of Ottawa · CAUniversity of Tennessee at Knoxville · USAgricultural Research Service · USDiversité, adaptation et développement des plantes · FRKunming University of Science and Technology · CN
Funding
Computational Methods for Genome Assembly, Transcript Assembly, and Variant DiscoveryR01HG006677 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI SALZBERG, STEVEN L. · 2011 to 2025
$10.7MNHGRI NIH HHS R01 HG006677NHGRI NIH HHS R01-HG006677
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.
Indexed as
Evolution, MolecularGene Regulatory NetworksGenetic MarkersGenome, PlantAnanasChromosome MappingEpigenomicsGene Expression Regulation, PlantGenomicsHigh-Throughput Nucleotide SequencingPhotosynthesisGenetic Markers
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