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Authors: 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

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 ? 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.

Journal: Nature genetics
DOI: 10.1038/ng.3435
Year: 2015

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