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ARS Home » Pacific West Area » Hilo, Hawaii » Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center » Tropical Plant Genetic Resources and Disease Research » Research » Publications at this Location » Publication #332374
Title: The pineapple genome and the evolution of CAM photosynthesis

Author
item MING, RAY - University Of Illinois
item VANBUREN, ROBERT - University Of Illinois
item YAI, CHING MAN - University Of Illinois
item TANG, HAIBAO - University Of Illinois
item SCHATZ, MICHAEL - Cold Spring Harbor Laboratory
item BOWERS, JOHN - University Of Georgia
item LYONS, ERIC - University Of Arizona
item WANG, MING-LI - Hawaii Agricultural Research Center
item CHEN, JUNG - University Of Hawaii
item BIGGERS, ERIC - Cold Spring Harbor Laboratory
item ZHANG, JISEN - University Of Illinois
item HUANG, LIXIAN - University Of Illinois
item ZHANG, LINGMAO - University Of Illinois
item MIAO, WENJING - University Of Illinois
item ZHANG, JIAN - University Of Illinois
item YE, ZHANGYAO - University Of Illinois
item MIAO, CHENYONG - University Of Illinois
item LIN, ZHICONG - University Of Illinois
item WANG, HAO - University Of Georgia
item ZHOU, HONGYE - University Of Georgia
item YIM, WON - University Of Nevada
item PRIEST, HENRY - Danforth Plant Science Center
item ZHENG, CHUNFANG - University Of Ottawa
item WOODHOUSE, MARGARET - University Of California
item EDGER, PATRICK - University Of California
item GUYOT, ROMAIN - Institute For Research And Development (IRD)
item GUO, HAO-BO - University Of Tennessee
item GUO, HONG - University Of Tennessee
item ZHENG, GUANGYONG - Chinese Academy Of Sciences
item SINGH, RATNESH - Texas A&M Agrilife
item SHARMA, ANUPMA - Texas A&M Agrilife
item MIN, XIANGJIA - Youngstown State University
item ZHENG, YUN - Non ARS Employee
item LEE, HAYAN - Cold Spring Harbor Laboratory
item GURTOWSKI, JAMES - Cold Spring Harbor Laboratory
item SEDLAZECK, FRITZ - Cold Spring Harbor Laboratory
item HARKESS, ALEX - University Of Georgia
item MCKAIN, MICHAEL - Danforth Plant Science Center
item LIAO, ZHENYANG - University Of Illinois
item FANG, JINGPING - University Of Illinois
item LIU, JUAN - University Of Illinois
item ZHANG, XIAODAN - University Of Illinois
item ZHANG, QING - University Of Illinois
item HU, WEICHANG - University Of Illinois
item QIN, YUAN - University Of Illinois
item WANG, KAI - University Of Illinois
item CHEN, LI-YU - University Of Illinois
item SHIRLEY, NEIL - University Of Adelaide
item LIN, YANN-RONG - National Taiwan University
item LIU, LI-YU - National Taiwan University
item HERNANDEZ, ALVARO - University Of Illinois
item WRIGHT, CHRIS - University Of Illinois
item BULONE, VINCENT - University Of Adelaide
item TUSKAN, GERALD - Oak Ridge National Laboratory
item HEATH, KATY - University Of Illinois
item Zee, Francis
item MOORE, PAUL - Hawaii Agricultural Research Center
item SUNKAR, RAMANJULU - Oklahoma State University
item LEEBENS-MACK, JAMES - University Of Georgia
item MOCKLER, TODD - Danforth Plant Science Center
item BENNETZEN, JEFFREY - University Of Georgia
item FREELING, MICHAEL - University Of California
item SANKOFF, DAVID - University Of Ottawa
item PATERSON, ANDREW - University Of Georgia
item ZHU, XINGUANG - Chinese Academy Of Sciences
item YANG, XIAOHAN - Oak Ridge National Laboratory
item SMITH, J ANDREW - University Of Oxford
item CUSHMAN, JOHN - University Of Nevada
item PAULL, ROBERT - University Of Hawaii
item YU, QINGYI - Texas A&M Agrilife

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/5/2015
Publication Date: 11/2/2015
Citation: Ming, R., Vanburen, R., Yai, C., Tang, H., Schatz, M., Bowers, J., Lyons, E., Wang, M., Chen, J., Biggers, E., Zhang, J., Huang, L., Zhang, L., Miao, W., Zhang, J., Ye, Z., Miao, C., Lin, Z., Wang, H., Zhou, H., Yim, W., Priest, H., Zheng, C., Woodhouse, M., Edger, P., Guyot, R., Guo, H., Guo, H., Zheng, G., Singh, R., Sharma, A., Min, X., Zheng, Y., Lee, H., Gurtowski, J., Sedlazeck, F., Harkess, A., Mckain, M., Liao, Z., Fang, J., Liu, J., Zhang, X., Zhang, Q., Hu, W., Qin, Y., Wang, K., Chen, L., Shirley, N., Lin, Y., Liu, L., Hernandez, A., Wright, C., Bulone, V., Tuskan, G., Heath, K., Zee, F.T., Moore, P., Sunkar, R., Leebens-Mack, J., Mockler, T., Bennetzen, J., Freeling, M., Sankoff, D., Paterson, A., Zhu, X., Yang, X., Smith, J., Cushman, J., Paull, R., Yu, Q. 2015. The pineapple genome and the evolution of CAM photosynthesis. Nature Genetics. 47: 1435-1442.

Interpretive Summary: Pineapple is the most economically important crop in the group of plants that conduct photosynthesis similar to cactus, called crassulacean acid metabolism (CAM). This pathway is important in water use efficiency where it takes up carbon dioxide at night when temperatures are cooler. The genomes from two commercial pineapple cultivars were sequenced and compared to a wild relative, Ananas bracteatus. The gene sequences revealed that photosynthesis in pineapple transitioned from C3 photosynthesis which is common in many dicot (non-grass) plants. The pineapple CAM photosynthesis evolved from genes associated with circadian rhythm and not through the genes introduced through crossing, development of novel gene functions or duplication of genes.

Technical 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 RHO duplication event. The pineapple lineage has transitioned from C3 photosynthesis to CAM, with CAM-related genes exhibiting a duel 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.