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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:
 [1];  [2];  [1]; ORCiD logo [3];  [4];  [5];  [6];  [7];  [8];  [4];  [9];  [9];  [9];  [9];  [9];  [9];  [9];  [9];  [5];  [5] more »;  [10];  [11];  [12];  [13];  [13];  [14];  [15];  [15];  [16]; ORCiD logo [17];  [17];  [18];  [19];  [4];  [4];  [4];  [5];  [11];  [9];  [9];  [9];  [9];  [9];  [9];  [9];  [9];  [9];  [20];  [21];  [21];  [22];  [22];  [20];  [23];  [24];  [25];  [7];  [26];  [5]; ORCiD logo [11];  [5];  [13];  [12];  [27];  [16];  [23]; ORCiD logo [28];  [10];  [8];  [17] « less
+ Show Author Affiliations
  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
Publication Date:
Research Org.:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC); National Science Foundation (NSF); National Institutes of Health (NIH)
OSTI Identifier:
1293938
Alternate Identifier(s):
OSTI ID: 1319239
Grant/Contract Number:  
SC0008834; 0922545; DBI-1401572; IOS-1444567; R01-HG006677; DBI-1350041; DBI-1265383; AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Nature Genetics
Additional Journal Information:
Journal Volume: 47; Journal Issue: 12; Journal ID: ISSN 1061-4036
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; DNA sequencing; Genomics; Plant genetics

Citation Formats

Ming, Ray, VanBuren, Robert, Wai, Ching Man, Tang, Haibao, Schatz, Michael C., Bowers, John E., Lyons, Eric, Wang, Ming-Li, Chen, Jung, Biggers, Eric, Zhang, Jisen, Huang, Lixian, Zhang, Lingmao, Miao, Wenjing, Zhang, Jian, Ye, Zhangyao, Miao, Chenyong, Lin, Zhicong, Wang, Hao, Zhou, Hongye, Yim, Won C., Priest, Henry D., Zheng, Chunfang, Woodhouse, Margaret, Edger, Patrick P., Guyot, Romain, Guo, Hao-Bo, Guo, Hong, Zheng, Guangyong, Singh, Ratnesh, Sharma, Anupma, Min, Xiangjia, Zheng, Yun, Lee, Hayan, Gurtowski, James, Sedlazeck, Fritz J., Harkess, Alex, McKain, Michael R., Liao, Zhenyang, Fang, Jingping, Liu, Juan, Zhang, Xiaodan, Zhang, Qing, Hu, Weichang, Qin, Yuan, Wang, Kai, Chen, Li-Yu, Shirley, Neil, Lin, Yann-Rong, Liu, Li-Yu, Hernandez, Alvaro G., Wright, Chris L., Bulone, Vincent, Tuskan, Gerald A., Heath, Katy, Zee, Francis, Moore, Paul H., Sunkar, Ramanjulu, Leebens-Mack, James H., Mockler, Todd, Bennetzen, Jeffrey L., Freeling, Michael, Sankoff, David, Paterson, Andrew H., Zhu, Xinguang, Yang, Xiaohan, Smith, J. Andrew C., Cushman, John C., Paull, Robert E., and Yu, Qingyi. The pineapple genome and the evolution of CAM photosynthesis. United States: N. p., 2015. Web. doi:10.1038/ng.3435.
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Ming, Ray, VanBuren, Robert, Wai, Ching Man, Tang, Haibao, Schatz, Michael C., Bowers, John E., Lyons, Eric, Wang, Ming-Li, Chen, Jung, Biggers, Eric, Zhang, Jisen, Huang, Lixian, Zhang, Lingmao, Miao, Wenjing, Zhang, Jian, Ye, Zhangyao, Miao, Chenyong, Lin, Zhicong, Wang, Hao, Zhou, Hongye, Yim, Won C., Priest, Henry D., Zheng, Chunfang, Woodhouse, Margaret, Edger, Patrick P., Guyot, Romain, Guo, Hao-Bo, Guo, Hong, Zheng, Guangyong, Singh, Ratnesh, Sharma, Anupma, Min, Xiangjia, Zheng, Yun, Lee, Hayan, Gurtowski, James, Sedlazeck, Fritz J., Harkess, Alex, McKain, Michael R., Liao, Zhenyang, Fang, Jingping, Liu, Juan, Zhang, Xiaodan, Zhang, Qing, Hu, Weichang, Qin, Yuan, Wang, Kai, Chen, Li-Yu, Shirley, Neil, Lin, Yann-Rong, Liu, Li-Yu, Hernandez, Alvaro G., Wright, Chris L., Bulone, Vincent, Tuskan, Gerald A., Heath, Katy, Zee, Francis, Moore, Paul H., Sunkar, Ramanjulu, Leebens-Mack, James H., Mockler, Todd, Bennetzen, Jeffrey L., Freeling, Michael, Sankoff, David, Paterson, Andrew H., Zhu, Xinguang, Yang, Xiaohan, Smith, J. Andrew C., Cushman, John C., Paull, Robert E., & Yu, Qingyi. The pineapple genome and the evolution of CAM photosynthesis. United States. https://doi.org/10.1038/ng.3435
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Ming, Ray, VanBuren, Robert, Wai, Ching Man, Tang, Haibao, Schatz, Michael C., Bowers, John E., Lyons, Eric, Wang, Ming-Li, Chen, Jung, Biggers, Eric, Zhang, Jisen, Huang, Lixian, Zhang, Lingmao, Miao, Wenjing, Zhang, Jian, Ye, Zhangyao, Miao, Chenyong, Lin, Zhicong, Wang, Hao, Zhou, Hongye, Yim, Won C., Priest, Henry D., Zheng, Chunfang, Woodhouse, Margaret, Edger, Patrick P., Guyot, Romain, Guo, Hao-Bo, Guo, Hong, Zheng, Guangyong, Singh, Ratnesh, Sharma, Anupma, Min, Xiangjia, Zheng, Yun, Lee, Hayan, Gurtowski, James, Sedlazeck, Fritz J., Harkess, Alex, McKain, Michael R., Liao, Zhenyang, Fang, Jingping, Liu, Juan, Zhang, Xiaodan, Zhang, Qing, Hu, Weichang, Qin, Yuan, Wang, Kai, Chen, Li-Yu, Shirley, Neil, Lin, Yann-Rong, Liu, Li-Yu, Hernandez, Alvaro G., Wright, Chris L., Bulone, Vincent, Tuskan, Gerald A., Heath, Katy, Zee, Francis, Moore, Paul H., Sunkar, Ramanjulu, Leebens-Mack, James H., Mockler, Todd, Bennetzen, Jeffrey L., Freeling, Michael, Sankoff, David, Paterson, Andrew H., Zhu, Xinguang, Yang, Xiaohan, Smith, J. Andrew C., Cushman, John C., Paull, Robert E., and Yu, Qingyi. Mon . "The pineapple genome and the evolution of CAM photosynthesis". United States. https://doi.org/10.1038/ng.3435. https://www.osti.gov/servlets/purl/1293938.
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@article{osti_1293938,
title = {The pineapple genome and the evolution of CAM photosynthesis},
author = {Ming, Ray and VanBuren, Robert and Wai, Ching Man and Tang, Haibao and Schatz, Michael C. and Bowers, John E. and Lyons, Eric and Wang, Ming-Li and Chen, Jung and Biggers, Eric and Zhang, Jisen and Huang, Lixian and Zhang, Lingmao and Miao, Wenjing and Zhang, Jian and Ye, Zhangyao and Miao, Chenyong and Lin, Zhicong and Wang, Hao and Zhou, Hongye and Yim, Won C. and Priest, Henry D. and Zheng, Chunfang and Woodhouse, Margaret and Edger, Patrick P. and Guyot, Romain and Guo, Hao-Bo and Guo, Hong and Zheng, Guangyong and Singh, Ratnesh and Sharma, Anupma and Min, Xiangjia and Zheng, Yun and Lee, Hayan and Gurtowski, James and Sedlazeck, Fritz J. and Harkess, Alex and McKain, Michael R. and Liao, Zhenyang and Fang, Jingping and Liu, Juan and Zhang, Xiaodan and Zhang, Qing and Hu, Weichang and Qin, Yuan and Wang, Kai and Chen, Li-Yu and Shirley, Neil and Lin, Yann-Rong and Liu, Li-Yu and Hernandez, Alvaro G. and Wright, Chris L. and Bulone, Vincent and Tuskan, Gerald A. and Heath, Katy and Zee, Francis and Moore, Paul H. and Sunkar, Ramanjulu and Leebens-Mack, James H. and Mockler, Todd and Bennetzen, Jeffrey L. and Freeling, Michael and Sankoff, David and Paterson, Andrew H. and Zhu, Xinguang and Yang, Xiaohan and Smith, J. Andrew C. and Cushman, John C. and Paull, Robert E. and Yu, Qingyi},
abstractNote = {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.},
doi = {10.1038/ng.3435},
journal = {Nature Genetics},
number = 12,
volume = 47,
place = {United States},
year = {2015},
month = {11}
}
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    Ammonium intensifies CAM photosynthesis and counteracts drought effects by increasing malate transport and antioxidant capacity in Guzmania monostachia
    journal, February 2018

    • Pereira, Paula Natália; Gaspar, Marília; Smith, J. Andrew C.
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    A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales species
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    The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism
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    The low-copy nuclear gene Agt1 as a novel DNA barcoding marker for Bromeliaceae
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    Correction to: Simple protoplast isolation system for gene expression and protein interaction studies in pineapple (Ananas comosus L.)
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    Genome-wide searches and molecular analyses highlight the unique evolutionary path of flavone synthase I (FNSI) in Apiaceae
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    Identification of microRNAs, phasiRNAs and Their Targets in Pineapple
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    Reconstructing the genome of the most recent common ancestor of flowering plants
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    • Murat, Florent; Armero, Alix; Pont, Caroline
    • Nature Genetics, Vol. 49, Issue 4
    • DOI: 10.1038/ng.3813

    The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism
    journal, December 2017

    Transcriptome Profiling of the Pineapple under Low Temperature to Facilitate Its Breeding for Cold Tolerance
    journal, September 2016

    Correction to: Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave
    journal, April 2019

    CMIP: a software package capable of reconstructing genome-wide regulatory networks using gene expression data
    journal, December 2016

    Altered Gene Regulatory Networks Are Associated With the Transition From C3 to Crassulacean Acid Metabolism in Erycina (Oncidiinae: Orchidaceae)
    journal, January 2019

    • Heyduk, Karolina; Hwang, Michelle; Albert, Victor
    • Frontiers in Plant Science, Vol. 9
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    The kinome of pineapple: catalog and insights into functions in crassulacean acid metabolism plants
    journal, September 2018

    AfAP2-1, An Age-Dependent Gene of Aechmea fasciata, Responds to Exogenous Ethylene Treatment
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    • Lei, Ming; Li, Zhi-Ying; Wang, Jia-Bin
    • International Journal of Molecular Sciences, Vol. 17, Issue 3
    • DOI: 10.3390/ijms17030303

    Gene duplication and evolution in recurring polyploidization–diploidization cycles in plants
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    Genome-Wide Comparative Analysis of Microsatellites in Pineapple
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    Genome-Wide Classification and Evolutionary and Functional Analyses of the VQ Family
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    Independent origin of MIRNA genes controlling homologous target genes by partial inverted duplication of antisense‐transcribed sequences
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    • Gramzow, Lydia; Lobbes, Dajana; Innard, Nathan
    • The Plant Journal, Vol. 101, Issue 2
    • DOI: 10.1111/tpj.14550

    Secrets of succulence
    journal, March 2017

    CMIP: a software package capable of reconstructing genome-wide regulatory networks using gene expression data
    journal, December 2016

    Expression Profiles of Wuschel-Related Homeobox Gene Family in Pineapple (Ananas comosus L)
    journal, November 2017

    Identification and evolution of C4 photosynthetic pathway genes in plants
    journal, March 2020

    Circadian Regulation of the Plant Transcriptome Under Natural Conditions
    journal, November 2019

    • Panter, Paige E.; Muranaka, Tomoaki; Cuitun-Coronado, David
    • Frontiers in Genetics, Vol. 10
    • DOI: 10.3389/fgene.2019.01239

    Temporal and spatial transcriptomic and micro RNA dynamics of CAM photosynthesis in pineapple
    journal, August 2017

    • Wai, Ching M.; VanBuren, Robert; Zhang, Jisen
    • The Plant Journal, Vol. 92, Issue 1
    • DOI: 10.1111/tpj.13630

    The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity
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    Virus-induced gene silencing: empowering genetics in non-model organisms
    journal, November 2018

    • Dommes, Anna B.; Gross, Thomas; Herbert, Denise B.
    • Journal of Experimental Botany, Vol. 70, Issue 3
    • DOI: 10.1093/jxb/ery411

    A role for MIR828 in pineapple fruit development
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    Photosynthesis and salinity: are these mutually exclusive?
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    A role for MIR828 in pineapple fruit development
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    The Apostasia genome and the evolution of orchids
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    • Zhang, Guo-Qiang; Liu, Ke-Wei; Li, Zhen
    • Nature, Vol. 549, Issue 7672
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    Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution
    journal, January 2019

    Simple protoplast isolation system for gene expression and protein interaction studies in pineapple (Ananas comosus L.)
    journal, October 2018

    Genome-Wide Analysis of the YABBY Transcription Factor Family in Pineapple and Functional Identification of AcYABBY4 Involvement in Salt Stress
    journal, November 2019

    • Li, Zeyun; Li, Gang; Cai, Mingxing
    • International Journal of Molecular Sciences, Vol. 20, Issue 23
    • DOI: 10.3390/ijms20235863

    The water lily genome and the early evolution of flowering plants
    journal, December 2019

    The asparagus genome sheds light on the origin and evolution of a young Y chromosome
    journal, November 2017

    Systematics of Vriesea (Bromeliaceae): phylogenetic relationships based on nuclear gene and partial plastome sequences
    journal, December 2019

    • Machado, Talita Mota; Loiseau, Oriane; Paris, Margot
    • Botanical Journal of the Linnean Society, Vol. 192, Issue 4
    • DOI: 10.1093/botlinnean/boz102

    Identification and characterization of pineapple leaf lncRNAs in crassulacean acid metabolism (CAM) photosynthesis pathway
    journal, April 2019

    Evolutionary history and structure of nuclear matrix constituent proteins, the plant analogues of lamins
    journal, March 2019

    • Ciska, Malgorzata; Hikida, Riku; Masuda, Kiyoshi
    • Journal of Experimental Botany, Vol. 70, Issue 10
    • DOI: 10.1093/jxb/erz102

    Gene duplication and evolution in recurring polyploidization–diploidization cycles in plants
    journal, February 2019

    Widespread lateral gene transfer among grasses
    journal, April 2021

    • Hibdige, Samuel G. S.; Raimondeau, Pauline; Christin, Pascal‐Antoine
    • New Phytologist, Vol. 230, Issue 6
    • DOI: 10.1111/nph.17328

    Genome-Wide Identification and Expression, Protein–Protein Interaction and Evolutionary Analysis of the Seed Plant-Specific BIG GRAIN and BIG GRAIN LIKE Gene Family
    journal, October 2017

    • Mishra, Bhuwaneshwar S.; Jamsheer K., Muhammed; Singh, Dhriti
    • Frontiers in Plant Science, Vol. 8
    • DOI: 10.3389/fpls.2017.01812

    Molecular foundations of chilling-tolerance of modern maize
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    Think tank: water relations of Bromeliaceae in their evolutionary context
    journal, April 2016

    • Males, Jamie
    • Botanical Journal of the Linnean Society, Vol. 181, Issue 3
    • DOI: 10.1111/boj.12423

    Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in Kalanchoë fedtschenkoi
    journal, August 2021

    • Moseley, Robert C.; Motta, Francis; Tuskan, Gerald A.
    • Cells, Vol. 10, Issue 9
    • DOI: 10.3390/cells10092217

    Time of day and network reprogramming during drought induced CAM photosynthesis in Sedum album
    journal, June 2019

    Comparative Analysis of GC Content Variations in Plant Genomes
    journal, April 2016

    Advances in and perspectives on evolution in Bromeliaceae
    journal, June 2016

    • Palma-Silva, Clarisse; Leal, Barbara S. S.; Chaves, Cleber J. N.
    • Botanical Journal of the Linnean Society, Vol. 181, Issue 3
    • DOI: 10.1111/boj.12431

    Identification, Characterization and Expression Profiles of Dof Transcription Factors in Pineapple (Ananas comosus L)
    journal, April 2018

    The evolutionary significance of polyploidy
    journal, May 2017

    • Van de Peer, Yves; Mizrachi, Eshchar; Marchal, Kathleen
    • Nature Reviews Genetics, Vol. 18, Issue 7
    • DOI: 10.1038/nrg.2017.26

    The Gastrodia elata genome provides insights into plant adaptation to heterotrophy
    journal, April 2018

    Analysis of MADS-box genes revealed modified flowering gene network and diurnal expression in pineapple
    journal, January 2020

    Agave angustifolia albino plantlets lose stomatal physiology function by changing the development of the stomatal complex due to a molecular disruption
    journal, January 2020

    • Sara, Hernández-Castellano; René, Garruña-Hernández; Rosa, Us-Camas
    • Molecular Genetics and Genomics, Vol. 295, Issue 3
    • DOI: 10.1007/s00438-019-01643-y

    Integrated DNA methylome and transcriptome analysis reveals the ethylene-induced flowering pathway genes in pineapple
    journal, December 2017

    A phylogenomic assessment of ancient polyploidy and genome evolution across the Poales
    journal, March 2016

    • McKain, Michael R.; Tang, Haibao; McNeal, Joel R.
    • Genome Biology and Evolution
    • DOI: 10.1093/gbe/evw060

    A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales species
    journal, August 2018

    • Munhoz, Carla Freitas; Costa, Zirlane Portugal; Cauz-Santos, Luiz Augusto
    • Scientific Reports, Vol. 8, Issue 1
    • DOI: 10.1038/s41598-018-31330-8

    Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis)
    journal, December 2019

    Mikania micrantha genome provides insights into the molecular mechanism of rapid growth
    journal, January 2020

    Origin and mechanism of crassulacean acid metabolism in orchids as implied by comparative transcriptomics and genomics of the carbon fixation pathway
    journal, April 2016

    • Zhang, Liangsheng; Chen, Fei; Zhang, Guo-Qiang
    • The Plant Journal, Vol. 86, Issue 2
    • DOI: 10.1111/tpj.13159

    The distance and median problems in the single-cut-or-join model with single-gene duplications
    journal, May 2020

    • Mane, Aniket C.; Lafond, Manuel; Feijao, Pedro C.
    • Algorithms for Molecular Biology, Vol. 15, Issue 1
    • DOI: 10.1186/s13015-020-00169-y

    PGD: Pineapple Genomics Database
    journal, September 2018

    New insights into the evolution and functional divergence of the SWEET family in Saccharum based on comparative genomics
    journal, November 2018

    Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA
    journal, February 2019

    Ancient Polyploidy and Genome Evolution in Palms
    journal, April 2019

    • Barrett, Craig F.; McKain, Michael R.; Sinn, Brandon T.
    • Genome Biology and Evolution, Vol. 11, Issue 5
    • DOI: 10.1093/gbe/evz092

    Histological evaluation of pineapple transgenic plants following 8 years of field growth
    journal, January 2020

    DArTseq Molecular Markers Associated with the Spiny-Tip Leaf Margin in Pineapple (Ananas comosus L.)
    journal, January 2020

    Economic importance, taxonomic representation and scientific priority as drivers of genome sequencing projects
    journal, November 2016

    • Vallée, Geneviève C.; Muñoz, Daniella Santos; Sankoff, David
    • BMC Genomics, Vol. 17, Issue S10
    • DOI: 10.1186/s12864-016-3100-9

    Time of day and network reprogramming during drought induced CAM photosynthesis in Sedum album
    journal, June 2019

    New insights into the evolution and functional divergence of the SWEET family in Saccharum based on comparative genomics
    journal, November 2018

    Comparative genomics can provide new insights into the evolutionary mechanisms and gene function in CAM plants
    journal, September 2019

    • Yang, Xiaohan; Liu, Degao; Tschaplinski, Timothy J.
    • Journal of Experimental Botany, Vol. 70, Issue 22
    • DOI: 10.1093/jxb/erz408

    Secrets of succulence
    text, January 2017

    Interaction between the Circadian Clock and Regulators of Heat Stress Responses in Plants
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    Developing naturally stress-resistant crops for a sustainable agriculture
    journal, November 2018

    Elucidating and mining the Tulipa and Lilium transcriptomes
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    • Moreno-Pachon, Natalia M.; Leeggangers, Hendrika A. C. F.; Nijveen, Harm
    • Plant Molecular Biology, Vol. 92, Issue 3
    • DOI: 10.1007/s11103-016-0508-1

    Detecting early signs of heat and drought stress in Phoenix dactylifera (date palm)
    journal, June 2017

    Genome Wide Identification and Expression Profiles of TALE Genes in Pineapple (Ananas comosus L)
    journal, June 2019

    Genome-Wide Identification and Expression Profile Analysis of WRKY Family Genes in the Autopolyploid Saccharum spontaneum
    journal, December 2019

    • Li, Zhen; Hua, Xiuting; Zhong, Weiming
    • Plant and Cell Physiology, Vol. 61, Issue 3
    • DOI: 10.1093/pcp/pcz227

    Comparative genomics revealed the gene evolution and functional divergence of magnesium transporter families in Saccharum
    journal, January 2019

    Mikania micrantha genome provides insights into the molecular mechanism of rapid growth
    journal, January 2020

    The bracteatus pineapple genome and domestication of clonally propagated crops
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    Ancient Polyploidy and Genome Evolution in Palms
    journal, April 2019

    • Barrett, Craig F.; McKain, Michael R.; Sinn, Brandon T.
    • Genome Biology and Evolution, Vol. 11, Issue 5
    • DOI: 10.1093/gbe/evz092

    The genetics of convergent evolution: insights from plant photosynthesis
    journal, March 2019

    • Heyduk, Karolina; Moreno-Villena, Jose J.; Gilman, Ian S.
    • Nature Reviews Genetics, Vol. 20, Issue 8
    • DOI: 10.1038/s41576-019-0107-5

    Plant evolution and environmental adaptation unveiled by long-read whole-genome sequencing of Spirodela
    journal, September 2019

    • An, Dong; Zhou, Yong; Li, Changsheng
    • Proceedings of the National Academy of Sciences, Vol. 116, Issue 38
    • DOI: 10.1073/pnas.1910401116

    Genome-Wide Analysis of the YABBY Transcription Factor Family in Pineapple and Functional Identification of AcYABBY4 Involvement in Salt Stress
    journal, November 2019

    • Li, Zeyun; Li, Gang; Cai, Mingxing
    • International Journal of Molecular Sciences, Vol. 20, Issue 23
    • DOI: 10.3390/ijms20235863

    The water lily genome and the early evolution of flowering plants
    journal, December 2019

    The Gastrodia elata genome provides insights into plant adaptation to heterotrophy
    journal, April 2018

    Evolutionary history and structure of nuclear matrix constituent proteins, the plant analogues of lamins
    journal, March 2019

    • Ciska, Malgorzata; Hikida, Riku; Masuda, Kiyoshi
    • Journal of Experimental Botany, Vol. 70, Issue 10
    • DOI: 10.1093/jxb/erz102

    Undervalued potential of crassulacean acid metabolism for current and future agricultural production
    journal, June 2019

    • Davis, Sarah C.; Simpson, June; Gil-Vega, Katia del Carmen
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    • DOI: 10.1093/jxb/erz223

    Expansin gene loss is a common occurrence during adaptation to an aquatic environment
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    • Hepler, Nathan K.; Bowman, Alexa; Carey, Robert E.
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    Model-Based Detection of Whole-Genome Duplications in a Phylogeny
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    Chromosome-level genome assembly, annotation and evolutionary analysis of the ornamental plant Asparagus setaceus
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    Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave
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    Diurnal Cycling Transcription Factors of Pineapple Revealed by Genome-Wide Annotation and Global Transcriptomic Analysis
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    The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity
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    A first glimpse at genes important to the Azolla–Nostoc symbiosis
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    Ecophysiology of constitutive and facultative CAM photosynthesis
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    Phylogenetic relationships among Ananas and related taxa (Bromelioideae, Bromeliaceae) based on nuclear, plastid and AFLP data
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    Genomic Survey, Characterization, and Expression Profile Analysis of the SBP Genes in Pineapple (Ananas comosus L.)
    journal, January 2017

    • Ali, Hina; Liu, Yanhui; Azam, Syed Muhammad
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    The role of cis-elements in the evolution of crassulacean acid metabolism photosynthesis
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    Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis)
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    • Hollender, Courtney A.; Kang, Chunying; Darwish, Omar
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    The asparagus genome sheds light on the origin and evolution of a young Y chromosome
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    RNA-seq transcriptomic profiling of crassulacean acid metabolism pathway in Dendrobium catenatum
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    Revisiting ancestral polyploidy in plants
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    • Ruprecht, Colin; Lohaus, Rolf; Vanneste, Kevin
    • Science Advances, Vol. 3, Issue 7
    • DOI: 10.1126/sciadv.1603195
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