The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism

Xiaohan Yang, Rongbin Hu, Hengfu Yin, Jerry Jenkins, Shengqiang Shu, Haibao Tang, Degao Liu, Deborah A. Weighill, Won Cheol Yim, Jungmin Ha, Karolina Heyduk, David M. Goodstein, Hao Bo Guo, Robert C. Moseley, Elisabeth Fitzek, Sara Jawdy, Zhihao Zhang, Meng Xie, James Hartwell, Jane GrimwoodPaul E. Abraham, Ritesh Mewalal, Juan D. Beltrán, Susanna F. Boxall, Louisa V. Dever, Kaitlin J. Palla, Rebecca Albion, Travis Garcia, Jesse A. Mayer, Sung Don Lim, Ching Man Wai, Paul Peluso, Robert Van Buren, Henrique Cestari De Paoli, Anne M. Borland, Hong Guo, Jin Gui Chen, Wellington Muchero, Yanbin Yin, Daniel A. Jacobson, Timothy J. Tschaplinski, Robert L. Hettich, Ray Ming, Klaus Winter, James H. Leebens-Mack, J. Andrew C. Smith, John C. Cushman, Jeremy Schmutz, Gerald A. Tuskan

Research output: Contribution to journalArticlepeer-review

76 Scopus citations

Abstract

Crassulacean acid metabolism (CAM) is a water-use efficient adaptation of photosynthesis that has evolved independently many times in diverse lineages of flowering plants. We hypothesize that convergent evolution of protein sequence and temporal gene expression underpins the independent emergences of CAM from C3 photosynthesis. To test this hypothesis, we generate a de novo genome assembly and genome-wide transcript expression data for Kalanchoë fedtschenkoi, an obligate CAM species within the core eudicots with a relatively small genome (~260 Mb). Our comparative analyses identify signatures of convergence in protein sequence and re-scheduling of diel transcript expression of genes involved in nocturnal CO2 fixation, stomatal movement, heat tolerance, circadian clock, and carbohydrate metabolism in K. fedtschenkoi and other CAM species in comparison with non-CAM species. These findings provide new insights into molecular convergence and building blocks of CAM and will facilitate CAM-into-C3 photosynthesis engineering to enhance water-use efficiency in crops.

Original languageEnglish (US)
Article number1899
JournalNature communications
Volume8
Issue number1
DOIs
StatePublished - Dec 1 2017
Externally publishedYes

Bibliographical note

Funding Information:
This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. This research was supported by the U.S. Department of Energy, Office of Science, Genomic Science Program under Award Number DE-SC0008834. Additional support was provided by the UK Biotechnology and Biological Sciences Research Council (grant no. BB/F009313/1) and the Laboratory Directed Research and Development (LDRD) Program (Project ID: 7758) of Oak Ridge National Laboratory. The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02–05CH11231. This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory. This research also used the Compute and Data Environment for Science (CADES) at the Oak Ridge National Laboratory. We thank Daniel Rokhsar, Mary Ann Cushman, and Lee Gunter for critical review and comments on the manuscript and Lori Kunder (Kunder Design Studio) for assistance with figure preparation. Oak Ridge National Laboratory is managed by UT-Battelle, LLC for the U.S. Department of Energy under Contract Number DE-AC05-00OR22725.

Publisher Copyright:
© 2017 The Author(s).

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