The pineapple genome and the evolution of CAM photosynthesis

Ray Ming*, Robert VanBuren, Ching Man Wai, Haibao Tang, Michael C. Schatz, John E. Bowers, Eric Lyons, Ming Li Wang, Jung Chen, Eric Biggers, Jisen Zhang, Lixian Huang, Lingmao Zhang, Wenjing Miao, Jian Zhang, Zhangyao Ye, Chenyong Miao, Zhicong Lin, Hao Wang, Hongye ZhouWon C. Yim, Henry D. Priest, Chunfang Zheng, Margaret Woodhouse, Patrick P. Edger, Romain Guyot, Hao Bo Guo, Hong Guo, Guangyong Zheng, Ratnesh Singh, Anupma Sharma, Xiangjia Min, Yun Zheng, Hayan Lee, James Gurtowski, Fritz J. Sedlazeck, Alex Harkess, Michael R. McKain, Zhenyang Liao, Jingping Fang, Juan Liu, Xiaodan Zhang, Qing Zhang, Weichang Hu, Yuan Qin, Kai Wang, Li Yu Chen, Neil Shirley, Yann Rong Lin, Li Yu Liu, Alvaro G. Hernandez, Chris L. Wright, Vincent Bulone, Gerald A. Tuskan, Katy Heath, Francis Zee, Paul H. Moore, Ramanjulu Sunkar, James H. Leebens-Mack, Todd Mockler, Jeffrey L. Bennetzen, Michael Freeling, David Sankoff, Andrew H. Paterson, Xinguang Zhu, Xiaohan Yang, J. Andrew C. Smith, John C. Cushman, Robert E. Paull, Qingyi Yu

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

395 Scopus citations


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 C 3 plants, through the regulatory neofunctionalization of preexisting genes and not through the acquisition of neofunctionalized genes via whole-genome or tandem gene duplication.

Original languageEnglish (US)
Pages (from-to)1435-1442
Number of pages8
JournalNature Genetics
Issue number12
StatePublished - Dec 1 2015
Externally publishedYes

ASJC Scopus subject areas

  • Genetics


Dive into the research topics of 'The pineapple genome and the evolution of CAM photosynthesis'. Together they form a unique fingerprint.

Cite this