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Title: The pineapple genome and the evolution of CAM photosynthesis

Journal Article · · Nature Genetics
DOI: https://doi.org/10.1038/ng.3435 · OSTI ID:1293938
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  1. Fujian Agriculture and Forestry Univ., Fuzhou (China); Univ. of Illinois, Urbana-Champaign, IL (United States). School of Integrative Biology Joint Center for Genomics and Biotechnology; Fujian Agriculture and Forestry Univ., Fuzhou (China). Fujian-Taiwan Joint Center for Ecological Control of Crop Pests; Univ. of Illinois, Urbana-Champaign, IL (United States). Dept. of Plant Biology
  2. Fujian Agriculture and Forestry Univ., Fuzhou (China); Univ. of Illinois, Urbana-Champaign, IL (United States). School of Integrative Biology Joint Center for Genomics and Biotechnology; Fujian Agriculture and Forestry Univ., Fuzhou (China). Fujian-Taiwan Joint Center for Ecological Control of Crop Pests; Univ. of Illinois, Urbana-Champaign, IL (United States). Dept. of Plant Biology; Donald Danforth Plant Science Center, St. Louis, MO (United States)
  3. Fujian Agriculture and Forestry Univ., Fuzhou (China); Univ. of Illinois, Urbana-Champaign, IL (United States). School of Integrative Biology Joint Center for Genomics and Biotechnology; Fujian Agriculture and Forestry Univ., Fuzhou (China). Fujian-Taiwan Joint Center for Ecological Control of Crop Pests; Univ. of Arizona, Tucson, AZ (United States). iPlant Collaborative
  4. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY (United States)
  5. Univ. of Georgia, Athens, GA (United States). Dept. of Plant Biology
  6. Univ. of Arizona, Tucson, AZ (United States). iPlant Collaborative
  7. Hawaii Agriculture Research Center, Kunia, HI (United States)
  8. Univ. of Hawaii, Honolulu, HI (United States). Dept. of Tropical Plant and Soil Sciences
  9. Fujian Agriculture and Forestry Univ., Fuzhou (China); Univ. of Illinois, Urbana-Champaign, IL (United States). School of Integrative Biology Joint Center for Genomics and Biotechnology; Fujian Agriculture and Forestry Univ., Fuzhou (China). Fujian-Taiwan Joint Center for Ecological Control of Crop Pests
  10. Univ. of Nevada, Reno, NV (United States). Dept. of Biochemistry and Molecular Biology
  11. Donald Danforth Plant Science Center, St. Louis, MO (United States)
  12. Univ. of Ottawa, Ottawa, ON (Canada). Dept. of Mathematics and Statistics
  13. Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology
  14. Inst. of Research for Development, Diversity and Adaptation of Plants Development, Montpellier (France)
  15. Univ. of Tennessee, Knoxville, TN (United States). Dept. of Biochemistry and Cellular and Molecular Biology
  16. Chinese Academy of Sciences - Max Planck Gesellschaft Partner Inst. for Computational Biology (CAS-MPG), Shanghai (China); Chinese Academy of Sciences (CAS), Shanghai (China). Shanghai Inst. for Biological Sciences
  17. Texas A&M Univ. System, Dallas, TX (United States). Dept. of Plant Pathology and Microbiology
  18. Youngstown State Univ., OH (United States). Dept. of Biological Sciences
  19. Kunming Univ. of Science and Technology, Kunming (China)
  20. Univ. of Adelaide, SA (Australia). Waite Campus Urrbrae, School of Agriculture, Food and Wine
  21. National Taiwan Univ., Taipei (Taiwan). Dept. of Agronomy
  22. Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States). W.M. Keck Center
  23. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division
  24. Univ. of Illinois, Urbana-Champaign, IL (United States). Dept. of Plant Biology
  25. US Dept. of Agriculture - Agricultural Research Service (USDA-ARS)., Hilo, HI (United States). Pacific Basin Agricultural Research Center
  26. Oklahoma State Univ., Stillwater, OK (United States). Dept. of Biochemistry and Molecular Biology
  27. Univ. of Georgia, Athens, GA (United States). Plant Genome Mapping Lab.
  28. Univ. of Oxford (United Kingdom). Dept. of Plant Sciences
+ Show Author Affiliations

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 Ļ 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. Lastly, we found 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.

Research Organization:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Organization:
USDOE Office of Science (SC); National Science Foundation (NSF); National Institutes of Health (NIH)
Grant/Contract Number:
SC0008834; 0922545; DBI-1401572; IOS-1444567; R01-HG006677; DBI-1350041; DBI-1265383; AC05-00OR22725
OSTI ID:
1293938
Alternate ID(s):
OSTI ID: 1319239
Journal Information:
Nature Genetics, Vol. 47, Issue 12; ISSN 1061-4036
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 349 works
Citation information provided by
Web of Science

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The low-copy nuclear gene Agt1 as a novel DNA barcoding marker for Bromeliaceae journal March 2020
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Additional file 1 of Identification and evolution of C4 photosynthetic pathway genes in plants dataset January 2020
Additional file 2 of Identification and evolution of C4 photosynthetic pathway genes in plants dataset January 2020
Additional file 3 of Identification and evolution of C4 photosynthetic pathway genes in plants dataset January 2020
Additional file 4 of Identification and evolution of C4 photosynthetic pathway genes in plants dataset January 2020
Additional file 5 of Identification and evolution of C4 photosynthetic pathway genes in plants image January 2020
Additional file 6 of Identification and evolution of C4 photosynthetic pathway genes in plants image January 2020
Additional file 7 of Identification and evolution of C4 photosynthetic pathway genes in plants image January 2020
Additional file 8 of Identification and evolution of C4 photosynthetic pathway genes in plants dataset January 2020
Additional file 9 of Identification and evolution of C4 photosynthetic pathway genes in plants dataset January 2020
Additional file 2 of Genome-wide study of pineapple (Ananas comosus L.) bHLH transcription factors indicates that cryptochrome-interacting bHLH2 (AcCIB2) participates in flowering time regulation and abiotic stress response image January 2020
Additional file 3 of Genome-wide study of pineapple (Ananas comosus L.) bHLH transcription factors indicates that cryptochrome-interacting bHLH2 (AcCIB2) participates in flowering time regulation and abiotic stress response image January 2020
Additional file 4 of Genome-wide study of pineapple (Ananas comosus L.) bHLH transcription factors indicates that cryptochrome-interacting bHLH2 (AcCIB2) participates in flowering time regulation and abiotic stress response dataset January 2020
Additional file 5 of Genome-wide study of pineapple (Ananas comosus L.) bHLH transcription factors indicates that cryptochrome-interacting bHLH2 (AcCIB2) participates in flowering time regulation and abiotic stress response image January 2020
Additional file 6 of Genome-wide study of pineapple (Ananas comosus L.) bHLH transcription factors indicates that cryptochrome-interacting bHLH2 (AcCIB2) participates in flowering time regulation and abiotic stress response dataset January 2020
Additional file 7 of Genome-wide study of pineapple (Ananas comosus L.) bHLH transcription factors indicates that cryptochrome-interacting bHLH2 (AcCIB2) participates in flowering time regulation and abiotic stress response dataset January 2020
Additional file 1 of Integrated analysis of DNA methylome and transcriptome reveals epigenetic regulation of CAM photosynthesis in pineapple dataset January 2021
Additional file 5 of Genome-wide identification and expression profiling of DREB genes in Saccharum spontaneum dataset January 2021
Additional file 14 of Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence dataset January 2021
Additional file 19 of Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence dataset January 2021
Additional file 3 of Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence dataset January 2021
Additional file 6 of Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence dataset January 2021
Additional file 2 of Comparative phylogenetic analysis of CBL reveals the gene family evolution and functional divergence in Saccharum spontaneum dataset January 2021
Additional file 3 of Comparative phylogenetic analysis of CBL reveals the gene family evolution and functional divergence in Saccharum spontaneum dataset January 2021
Additional file 4 of Comparative phylogenetic analysis of CBL reveals the gene family evolution and functional divergence in Saccharum spontaneum dataset January 2021
Additional file 5 of Comparative phylogenetic analysis of CBL reveals the gene family evolution and functional divergence in Saccharum spontaneum dataset January 2021
Additional file 6 of Comparative phylogenetic analysis of CBL reveals the gene family evolution and functional divergence in Saccharum spontaneum dataset January 2021
Additional file 7 of Comparative phylogenetic analysis of CBL reveals the gene family evolution and functional divergence in Saccharum spontaneum dataset January 2021
Additional file 10 of High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height dataset January 2021
Additional file 11 of High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height dataset January 2021
Additional file 12 of High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height dataset January 2021
Additional file 13 of High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height dataset January 2021
Additional file 14 of High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height dataset January 2021
Additional file 15 of High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height dataset January 2021
Additional file 17 of High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height dataset January 2021
Additional file 18 of High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height dataset January 2021
Additional file 19 of High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height dataset January 2021
Additional file 20 of High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height dataset January 2021
Additional file 21 of High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height dataset January 2021
Additional file 22 of High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height dataset January 2021
Additional file 23 of High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height dataset January 2021
Additional file 2 of High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height dataset January 2021
Additional file 3 of High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height dataset January 2021
Additional file 4 of High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height dataset January 2021
Additional file 5 of High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height dataset January 2021
Additional file 6 of High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height dataset January 2021
Additional file 7 of High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height dataset January 2021
Additional file 8 of High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height dataset January 2021
Additional file 9 of High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height dataset January 2021
Additional file 10 of Evolution and functional diversification of catalase genes in the green lineage dataset January 2022
Additional file 11 of Evolution and functional diversification of catalase genes in the green lineage dataset January 2022
Additional file 12 of Evolution and functional diversification of catalase genes in the green lineage dataset January 2022
Additional file 1 of Evolution and functional diversification of catalase genes in the green lineage image January 2022
Additional file 2 of Evolution and functional diversification of catalase genes in the green lineage image January 2022
Additional file 3 of Evolution and functional diversification of catalase genes in the green lineage image January 2022
Additional file 4 of Evolution and functional diversification of catalase genes in the green lineage image January 2022
Additional file 6 of Evolution and functional diversification of catalase genes in the green lineage dataset January 2022
Additional file 7 of Evolution and functional diversification of catalase genes in the green lineage dataset January 2022
Additional file 8 of Evolution and functional diversification of catalase genes in the green lineage dataset January 2022
Additional file 9 of Evolution and functional diversification of catalase genes in the green lineage dataset January 2022
Additional file 2 of Genome-wide characterization and expression analysis of the growth-regulating factor family in Saccharum dataset January 2022
Additional file 3 of Genome-wide characterization and expression analysis of the growth-regulating factor family in Saccharum dataset January 2022
Additional file 4 of Genome-wide characterization and expression analysis of the growth-regulating factor family in Saccharum dataset January 2022
Additional file 5 of Genome-wide characterization and expression analysis of the growth-regulating factor family in Saccharum dataset January 2022
Additional file 2 of Characterization and expression profiles of the B-box gene family during plant growth and under low-nitrogen stress in Saccharum dataset January 2023
Additional file 3 of Characterization and expression profiles of the B-box gene family during plant growth and under low-nitrogen stress in Saccharum dataset January 2023
Additional file 4 of Characterization and expression profiles of the B-box gene family during plant growth and under low-nitrogen stress in Saccharum dataset January 2023
Additional file 5 of Characterization and expression profiles of the B-box gene family during plant growth and under low-nitrogen stress in Saccharum dataset January 2023
Additional file 6 of Characterization and expression profiles of the B-box gene family during plant growth and under low-nitrogen stress in Saccharum dataset January 2023
Additional file 7 of Characterization and expression profiles of the B-box gene family during plant growth and under low-nitrogen stress in Saccharum dataset January 2023

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DNA sequencing
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