The pineapple genome and the evolution of CAM photosynthesis

作者：Ray Ming, Robert VanBuren, Ching Man Wai, Haibao Tang, Michael C. Schatz, John 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 Zhou, Won Cheol Yim, Henry D. Priest, Chunfang Zheng, Margaret Woodhouse, Patrick P. Edger, Romain Guyot, Hao‐Bo Guo, Hong Guo, Guangyong Zheng, Ratnesh Singh, Anupma Sharma, Xiang Jia 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 J. Shirley, Yann‐Rong Lin, Liyu Liu, Alvaro G. Hernandez, Chris Wright, Vincent Bulone, Gerald A. Tuskan, Katy D. Heath, Francis Zee, Paul H. Moore, Ramanjulu Sunkar, James H Leebens-Mack, Todd C. Mockler, Jeffrey L. Bennetzen, Michael Freeling, David Sankoff, Andrew H. Paterson, Xin‐Guang Zhu, Xiaohan Yang, J. Andrew C. Smith, John C. Cushman, Robert E. Paull, Qingyi Yu · 发表于：Nature Genetics · 年份：2015 · DOI：10.1038/ng.3435 · 被引用次数：757 · 研究领域：Photosynthetic Processes and Mechanisms、Genomics and Phylogenetic Studies、Chromosomal and Genetic Variations

Ray Ming, Robert Paull, Qingyi Yu and colleagues report the genome sequences of two cultivated pineapple varieties and one wild pineapple relative. Their analysis supports the use of the pineapple as a reference genome for monocot comparative genomics and provides insight into the evolution of crassulacean acid metabolism photosynthesis. 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 gen...