The pineapple genome and the evolution of CAM photosynthesis.
Identifieur interne : 002610 ( PubMed/Corpus ); précédent : 002609; suivant : 002611The pineapple genome and the evolution of CAM photosynthesis.
Auteurs : 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 Zhou ; Won 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 YuSource :
- Nature genetics [ 1546-1718 ] ; 2015.
English descriptors
- KwdEn :
- MESH :
- chemical : Genetic Markers.
- genetics : Ananas.
- methods : Genomics, High-Throughput Nucleotide Sequencing.
- physiology : Photosynthesis.
- Chromosome Mapping, Epigenomics, Evolution, Molecular, Gene Expression Regulation, Plant, Gene Regulatory Networks, Genome, Plant.
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 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 gene duplication.
DOI: 10.1038/ng.3435
PubMed: 26523774
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pubmed:26523774Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The pineapple genome and the evolution of CAM photosynthesis.</title><author><name sortKey="Ming, Ray" sort="Ming, Ray" uniqKey="Ming R" first="Ray" last="Ming">Ray Ming</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Vanburen, Robert" sort="Vanburen, Robert" uniqKey="Vanburen R" first="Robert" last="Vanburen">Robert Vanburen</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wai, Ching Man" sort="Wai, Ching Man" uniqKey="Wai C" first="Ching Man" last="Wai">Ching Man Wai</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Tang, Haibao" sort="Tang, Haibao" uniqKey="Tang H" first="Haibao" last="Tang">Haibao Tang</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Schatz, Michael C" sort="Schatz, Michael C" uniqKey="Schatz M" first="Michael C" last="Schatz">Michael C. Schatz</name><affiliation><nlm:affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Bowers, John E" sort="Bowers, John E" uniqKey="Bowers J" first="John E" last="Bowers">John E. Bowers</name><affiliation><nlm:affiliation>Department of Plant Biology, University of Georgia, Athens, Georgia, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Lyons, Eric" sort="Lyons, Eric" uniqKey="Lyons E" first="Eric" last="Lyons">Eric Lyons</name><affiliation><nlm:affiliation>iPlant Collaborative/University of Arizona, Tucson, Arizona, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Ming Li" sort="Wang, Ming Li" uniqKey="Wang M" first="Ming-Li" last="Wang">Ming-Li Wang</name><affiliation><nlm:affiliation>Hawaii Agriculture Research Center, Kunia, Hawaii, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Chen, Jung" sort="Chen, Jung" uniqKey="Chen J" first="Jung" last="Chen">Jung Chen</name><affiliation><nlm:affiliation>Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, Hawaii, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Biggers, Eric" sort="Biggers, Eric" uniqKey="Biggers E" first="Eric" last="Biggers">Eric Biggers</name><affiliation><nlm:affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Jisen" sort="Zhang, Jisen" uniqKey="Zhang J" first="Jisen" last="Zhang">Jisen Zhang</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Huang, Lixian" sort="Huang, Lixian" uniqKey="Huang L" first="Lixian" last="Huang">Lixian Huang</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Lingmao" sort="Zhang, Lingmao" uniqKey="Zhang L" first="Lingmao" last="Zhang">Lingmao Zhang</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Miao, Wenjing" sort="Miao, Wenjing" uniqKey="Miao W" first="Wenjing" last="Miao">Wenjing Miao</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Jian" sort="Zhang, Jian" uniqKey="Zhang J" first="Jian" last="Zhang">Jian Zhang</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Ye, Zhangyao" sort="Ye, Zhangyao" uniqKey="Ye Z" first="Zhangyao" last="Ye">Zhangyao Ye</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Miao, Chenyong" sort="Miao, Chenyong" uniqKey="Miao C" first="Chenyong" last="Miao">Chenyong Miao</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Lin, Zhicong" sort="Lin, Zhicong" uniqKey="Lin Z" first="Zhicong" last="Lin">Zhicong Lin</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Hao" sort="Wang, Hao" uniqKey="Wang H" first="Hao" last="Wang">Hao Wang</name><affiliation><nlm:affiliation>Department of Plant Biology, University of Georgia, Athens, Georgia, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zhou, Hongye" sort="Zhou, Hongye" uniqKey="Zhou H" first="Hongye" last="Zhou">Hongye Zhou</name><affiliation><nlm:affiliation>Department of Plant Biology, University of Georgia, Athens, Georgia, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Yim, Won C" sort="Yim, Won C" uniqKey="Yim W" first="Won C" last="Yim">Won C. Yim</name><affiliation><nlm:affiliation>Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Priest, Henry D" sort="Priest, Henry D" uniqKey="Priest H" first="Henry D" last="Priest">Henry D. Priest</name><affiliation><nlm:affiliation>Donald Danforth Plant Science Center, St. Louis, Missouri, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zheng, Chunfang" sort="Zheng, Chunfang" uniqKey="Zheng C" first="Chunfang" last="Zheng">Chunfang Zheng</name><affiliation><nlm:affiliation>Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Woodhouse, Margaret" sort="Woodhouse, Margaret" uniqKey="Woodhouse M" first="Margaret" last="Woodhouse">Margaret Woodhouse</name><affiliation><nlm:affiliation>Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Edger, Patrick P" sort="Edger, Patrick P" uniqKey="Edger P" first="Patrick P" last="Edger">Patrick P. Edger</name><affiliation><nlm:affiliation>Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Guyot, Romain" sort="Guyot, Romain" uniqKey="Guyot R" first="Romain" last="Guyot">Romain Guyot</name><affiliation><nlm:affiliation>Institut de Recherche pour le Développement, Diversité Adaptation et Développement des Plantes, Montpellier, France.</nlm:affiliation></affiliation></author><author><name sortKey="Guo, Hao Bo" sort="Guo, Hao Bo" uniqKey="Guo H" first="Hao-Bo" last="Guo">Hao-Bo Guo</name><affiliation><nlm:affiliation>Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Guo, Hong" sort="Guo, Hong" uniqKey="Guo H" first="Hong" last="Guo">Hong Guo</name><affiliation><nlm:affiliation>Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zheng, Guangyong" sort="Zheng, Guangyong" uniqKey="Zheng G" first="Guangyong" last="Zheng">Guangyong Zheng</name><affiliation><nlm:affiliation>Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Gesellschaft Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.</nlm:affiliation></affiliation></author><author><name sortKey="Singh, Ratnesh" sort="Singh, Ratnesh" uniqKey="Singh R" first="Ratnesh" last="Singh">Ratnesh Singh</name><affiliation><nlm:affiliation>Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, Texas, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Sharma, Anupma" sort="Sharma, Anupma" uniqKey="Sharma A" first="Anupma" last="Sharma">Anupma Sharma</name><affiliation><nlm:affiliation>Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, Texas, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Min, Xiangjia" sort="Min, Xiangjia" uniqKey="Min X" first="Xiangjia" last="Min">Xiangjia Min</name><affiliation><nlm:affiliation>Department of Biological Sciences, Youngstown State University, Youngstown, Ohio, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zheng, Yun" sort="Zheng, Yun" uniqKey="Zheng Y" first="Yun" last="Zheng">Yun Zheng</name><affiliation><nlm:affiliation>Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.</nlm:affiliation></affiliation></author><author><name sortKey="Lee, Hayan" sort="Lee, Hayan" uniqKey="Lee H" first="Hayan" last="Lee">Hayan Lee</name><affiliation><nlm:affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Gurtowski, James" sort="Gurtowski, James" uniqKey="Gurtowski J" first="James" last="Gurtowski">James Gurtowski</name><affiliation><nlm:affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Sedlazeck, Fritz J" sort="Sedlazeck, Fritz J" uniqKey="Sedlazeck F" first="Fritz J" last="Sedlazeck">Fritz J. Sedlazeck</name><affiliation><nlm:affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Harkess, Alex" sort="Harkess, Alex" uniqKey="Harkess A" first="Alex" last="Harkess">Alex Harkess</name><affiliation><nlm:affiliation>Department of Plant Biology, University of Georgia, Athens, Georgia, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Mckain, Michael R" sort="Mckain, Michael R" uniqKey="Mckain M" first="Michael R" last="Mckain">Michael R. Mckain</name><affiliation><nlm:affiliation>Donald Danforth Plant Science Center, St. Louis, Missouri, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Liao, Zhenyang" sort="Liao, Zhenyang" uniqKey="Liao Z" first="Zhenyang" last="Liao">Zhenyang Liao</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Fang, Jingping" sort="Fang, Jingping" uniqKey="Fang J" first="Jingping" last="Fang">Jingping Fang</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Liu, Juan" sort="Liu, Juan" uniqKey="Liu J" first="Juan" last="Liu">Juan Liu</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Xiaodan" sort="Zhang, Xiaodan" uniqKey="Zhang X" first="Xiaodan" last="Zhang">Xiaodan Zhang</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Qing" sort="Zhang, Qing" uniqKey="Zhang Q" first="Qing" last="Zhang">Qing Zhang</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Hu, Weichang" sort="Hu, Weichang" uniqKey="Hu W" first="Weichang" last="Hu">Weichang Hu</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Qin, Yuan" sort="Qin, Yuan" uniqKey="Qin Y" first="Yuan" last="Qin">Yuan Qin</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Kai" sort="Wang, Kai" uniqKey="Wang K" first="Kai" last="Wang">Kai Wang</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Chen, Li Yu" sort="Chen, Li Yu" uniqKey="Chen L" first="Li-Yu" last="Chen">Li-Yu Chen</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Shirley, Neil" sort="Shirley, Neil" uniqKey="Shirley N" first="Neil" last="Shirley">Neil Shirley</name><affiliation><nlm:affiliation>Australian Research Council (ARC) Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus Urrbrae, Adelaide, South Australia, Australia.</nlm:affiliation></affiliation></author><author><name sortKey="Lin, Yann Rong" sort="Lin, Yann Rong" uniqKey="Lin Y" first="Yann-Rong" last="Lin">Yann-Rong Lin</name><affiliation><nlm:affiliation>Department of Agronomy, National Taiwan University, Taipei, Taiwan.</nlm:affiliation></affiliation></author><author><name sortKey="Liu, Li Yu" sort="Liu, Li Yu" uniqKey="Liu L" first="Li-Yu" last="Liu">Li-Yu Liu</name><affiliation><nlm:affiliation>Department of Agronomy, National Taiwan University, Taipei, Taiwan.</nlm:affiliation></affiliation></author><author><name sortKey="Hernandez, Alvaro G" sort="Hernandez, Alvaro G" uniqKey="Hernandez A" first="Alvaro G" last="Hernandez">Alvaro G. Hernandez</name><affiliation><nlm:affiliation>W.M. Keck Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Wright, Chris L" sort="Wright, Chris L" uniqKey="Wright C" first="Chris L" last="Wright">Chris L. Wright</name><affiliation><nlm:affiliation>W.M. Keck Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Bulone, Vincent" sort="Bulone, Vincent" uniqKey="Bulone V" first="Vincent" last="Bulone">Vincent Bulone</name><affiliation><nlm:affiliation>Australian Research Council (ARC) Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus Urrbrae, Adelaide, South Australia, Australia.</nlm:affiliation></affiliation></author><author><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name><affiliation><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Heath, Katy" sort="Heath, Katy" uniqKey="Heath K" first="Katy" last="Heath">Katy Heath</name><affiliation><nlm:affiliation>Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zee, Francis" sort="Zee, Francis" uniqKey="Zee F" first="Francis" last="Zee">Francis Zee</name><affiliation><nlm:affiliation>US Department of Agriculture-Agricultural Research Service (USDA-ARS), Pacific Basin Agricultural Research Center, Hilo, Hawaii, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Moore, Paul H" sort="Moore, Paul H" uniqKey="Moore P" first="Paul H" last="Moore">Paul H. Moore</name><affiliation><nlm:affiliation>Hawaii Agriculture Research Center, Kunia, Hawaii, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Sunkar, Ramanjulu" sort="Sunkar, Ramanjulu" uniqKey="Sunkar R" first="Ramanjulu" last="Sunkar">Ramanjulu Sunkar</name><affiliation><nlm:affiliation>Department of Biochemistry and Molecular Biology, Noble Research Center, Oklahoma State University, Stillwater, Oklahoma, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Leebens Mack, James H" sort="Leebens Mack, James H" uniqKey="Leebens Mack J" first="James H" last="Leebens-Mack">James H. Leebens-Mack</name><affiliation><nlm:affiliation>Department of Plant Biology, University of Georgia, Athens, Georgia, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Mockler, Todd" sort="Mockler, Todd" uniqKey="Mockler T" first="Todd" last="Mockler">Todd Mockler</name><affiliation><nlm:affiliation>Donald Danforth Plant Science Center, St. Louis, Missouri, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Bennetzen, Jeffrey L" sort="Bennetzen, Jeffrey L" uniqKey="Bennetzen J" first="Jeffrey L" last="Bennetzen">Jeffrey L. Bennetzen</name><affiliation><nlm:affiliation>Department of Plant Biology, University of Georgia, Athens, Georgia, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Freeling, Michael" sort="Freeling, Michael" uniqKey="Freeling M" first="Michael" last="Freeling">Michael Freeling</name><affiliation><nlm:affiliation>Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Sankoff, David" sort="Sankoff, David" uniqKey="Sankoff D" first="David" last="Sankoff">David Sankoff</name><affiliation><nlm:affiliation>Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Paterson, Andrew H" sort="Paterson, Andrew H" uniqKey="Paterson A" first="Andrew H" last="Paterson">Andrew H. Paterson</name><affiliation><nlm:affiliation>Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zhu, Xinguang" sort="Zhu, Xinguang" uniqKey="Zhu X" first="Xinguang" last="Zhu">Xinguang Zhu</name><affiliation><nlm:affiliation>Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Gesellschaft Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.</nlm:affiliation></affiliation></author><author><name sortKey="Yang, Xiaohan" sort="Yang, Xiaohan" uniqKey="Yang X" first="Xiaohan" last="Yang">Xiaohan Yang</name><affiliation><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Smith, J Andrew C" sort="Smith, J Andrew C" uniqKey="Smith J" first="J Andrew C" last="Smith">J Andrew C. Smith</name><affiliation><nlm:affiliation>Department of Plant Sciences, University of Oxford, Oxford, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Cushman, John C" sort="Cushman, John C" uniqKey="Cushman J" first="John C" last="Cushman">John C. Cushman</name><affiliation><nlm:affiliation>Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Paull, Robert E" sort="Paull, Robert E" uniqKey="Paull R" first="Robert E" last="Paull">Robert E. Paull</name><affiliation><nlm:affiliation>Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, Hawaii, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Yu, Qingyi" sort="Yu, Qingyi" uniqKey="Yu Q" first="Qingyi" last="Yu">Qingyi Yu</name><affiliation><nlm:affiliation>Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, Texas, USA.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:26523774</idno><idno type="pmid">26523774</idno><idno type="doi">10.1038/ng.3435</idno><idno type="wicri:Area/PubMed/Corpus">002610</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002610</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">The pineapple genome and the evolution of CAM photosynthesis.</title><author><name sortKey="Ming, Ray" sort="Ming, Ray" uniqKey="Ming R" first="Ray" last="Ming">Ray Ming</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Vanburen, Robert" sort="Vanburen, Robert" uniqKey="Vanburen R" first="Robert" last="Vanburen">Robert Vanburen</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wai, Ching Man" sort="Wai, Ching Man" uniqKey="Wai C" first="Ching Man" last="Wai">Ching Man Wai</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Tang, Haibao" sort="Tang, Haibao" uniqKey="Tang H" first="Haibao" last="Tang">Haibao Tang</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Schatz, Michael C" sort="Schatz, Michael C" uniqKey="Schatz M" first="Michael C" last="Schatz">Michael C. Schatz</name><affiliation><nlm:affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Bowers, John E" sort="Bowers, John E" uniqKey="Bowers J" first="John E" last="Bowers">John E. Bowers</name><affiliation><nlm:affiliation>Department of Plant Biology, University of Georgia, Athens, Georgia, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Lyons, Eric" sort="Lyons, Eric" uniqKey="Lyons E" first="Eric" last="Lyons">Eric Lyons</name><affiliation><nlm:affiliation>iPlant Collaborative/University of Arizona, Tucson, Arizona, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Ming Li" sort="Wang, Ming Li" uniqKey="Wang M" first="Ming-Li" last="Wang">Ming-Li Wang</name><affiliation><nlm:affiliation>Hawaii Agriculture Research Center, Kunia, Hawaii, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Chen, Jung" sort="Chen, Jung" uniqKey="Chen J" first="Jung" last="Chen">Jung Chen</name><affiliation><nlm:affiliation>Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, Hawaii, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Biggers, Eric" sort="Biggers, Eric" uniqKey="Biggers E" first="Eric" last="Biggers">Eric Biggers</name><affiliation><nlm:affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Jisen" sort="Zhang, Jisen" uniqKey="Zhang J" first="Jisen" last="Zhang">Jisen Zhang</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Huang, Lixian" sort="Huang, Lixian" uniqKey="Huang L" first="Lixian" last="Huang">Lixian Huang</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Lingmao" sort="Zhang, Lingmao" uniqKey="Zhang L" first="Lingmao" last="Zhang">Lingmao Zhang</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Miao, Wenjing" sort="Miao, Wenjing" uniqKey="Miao W" first="Wenjing" last="Miao">Wenjing Miao</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Jian" sort="Zhang, Jian" uniqKey="Zhang J" first="Jian" last="Zhang">Jian Zhang</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Ye, Zhangyao" sort="Ye, Zhangyao" uniqKey="Ye Z" first="Zhangyao" last="Ye">Zhangyao Ye</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Miao, Chenyong" sort="Miao, Chenyong" uniqKey="Miao C" first="Chenyong" last="Miao">Chenyong Miao</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Lin, Zhicong" sort="Lin, Zhicong" uniqKey="Lin Z" first="Zhicong" last="Lin">Zhicong Lin</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Hao" sort="Wang, Hao" uniqKey="Wang H" first="Hao" last="Wang">Hao Wang</name><affiliation><nlm:affiliation>Department of Plant Biology, University of Georgia, Athens, Georgia, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zhou, Hongye" sort="Zhou, Hongye" uniqKey="Zhou H" first="Hongye" last="Zhou">Hongye Zhou</name><affiliation><nlm:affiliation>Department of Plant Biology, University of Georgia, Athens, Georgia, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Yim, Won C" sort="Yim, Won C" uniqKey="Yim W" first="Won C" last="Yim">Won C. Yim</name><affiliation><nlm:affiliation>Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Priest, Henry D" sort="Priest, Henry D" uniqKey="Priest H" first="Henry D" last="Priest">Henry D. Priest</name><affiliation><nlm:affiliation>Donald Danforth Plant Science Center, St. Louis, Missouri, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zheng, Chunfang" sort="Zheng, Chunfang" uniqKey="Zheng C" first="Chunfang" last="Zheng">Chunfang Zheng</name><affiliation><nlm:affiliation>Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Woodhouse, Margaret" sort="Woodhouse, Margaret" uniqKey="Woodhouse M" first="Margaret" last="Woodhouse">Margaret Woodhouse</name><affiliation><nlm:affiliation>Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Edger, Patrick P" sort="Edger, Patrick P" uniqKey="Edger P" first="Patrick P" last="Edger">Patrick P. Edger</name><affiliation><nlm:affiliation>Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Guyot, Romain" sort="Guyot, Romain" uniqKey="Guyot R" first="Romain" last="Guyot">Romain Guyot</name><affiliation><nlm:affiliation>Institut de Recherche pour le Développement, Diversité Adaptation et Développement des Plantes, Montpellier, France.</nlm:affiliation></affiliation></author><author><name sortKey="Guo, Hao Bo" sort="Guo, Hao Bo" uniqKey="Guo H" first="Hao-Bo" last="Guo">Hao-Bo Guo</name><affiliation><nlm:affiliation>Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Guo, Hong" sort="Guo, Hong" uniqKey="Guo H" first="Hong" last="Guo">Hong Guo</name><affiliation><nlm:affiliation>Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zheng, Guangyong" sort="Zheng, Guangyong" uniqKey="Zheng G" first="Guangyong" last="Zheng">Guangyong Zheng</name><affiliation><nlm:affiliation>Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Gesellschaft Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.</nlm:affiliation></affiliation></author><author><name sortKey="Singh, Ratnesh" sort="Singh, Ratnesh" uniqKey="Singh R" first="Ratnesh" last="Singh">Ratnesh Singh</name><affiliation><nlm:affiliation>Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, Texas, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Sharma, Anupma" sort="Sharma, Anupma" uniqKey="Sharma A" first="Anupma" last="Sharma">Anupma Sharma</name><affiliation><nlm:affiliation>Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, Texas, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Min, Xiangjia" sort="Min, Xiangjia" uniqKey="Min X" first="Xiangjia" last="Min">Xiangjia Min</name><affiliation><nlm:affiliation>Department of Biological Sciences, Youngstown State University, Youngstown, Ohio, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zheng, Yun" sort="Zheng, Yun" uniqKey="Zheng Y" first="Yun" last="Zheng">Yun Zheng</name><affiliation><nlm:affiliation>Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.</nlm:affiliation></affiliation></author><author><name sortKey="Lee, Hayan" sort="Lee, Hayan" uniqKey="Lee H" first="Hayan" last="Lee">Hayan Lee</name><affiliation><nlm:affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Gurtowski, James" sort="Gurtowski, James" uniqKey="Gurtowski J" first="James" last="Gurtowski">James Gurtowski</name><affiliation><nlm:affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Sedlazeck, Fritz J" sort="Sedlazeck, Fritz J" uniqKey="Sedlazeck F" first="Fritz J" last="Sedlazeck">Fritz J. Sedlazeck</name><affiliation><nlm:affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Harkess, Alex" sort="Harkess, Alex" uniqKey="Harkess A" first="Alex" last="Harkess">Alex Harkess</name><affiliation><nlm:affiliation>Department of Plant Biology, University of Georgia, Athens, Georgia, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Mckain, Michael R" sort="Mckain, Michael R" uniqKey="Mckain M" first="Michael R" last="Mckain">Michael R. Mckain</name><affiliation><nlm:affiliation>Donald Danforth Plant Science Center, St. Louis, Missouri, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Liao, Zhenyang" sort="Liao, Zhenyang" uniqKey="Liao Z" first="Zhenyang" last="Liao">Zhenyang Liao</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Fang, Jingping" sort="Fang, Jingping" uniqKey="Fang J" first="Jingping" last="Fang">Jingping Fang</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Liu, Juan" sort="Liu, Juan" uniqKey="Liu J" first="Juan" last="Liu">Juan Liu</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Xiaodan" sort="Zhang, Xiaodan" uniqKey="Zhang X" first="Xiaodan" last="Zhang">Xiaodan Zhang</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Qing" sort="Zhang, Qing" uniqKey="Zhang Q" first="Qing" last="Zhang">Qing Zhang</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Hu, Weichang" sort="Hu, Weichang" uniqKey="Hu W" first="Weichang" last="Hu">Weichang Hu</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Qin, Yuan" sort="Qin, Yuan" uniqKey="Qin Y" first="Yuan" last="Qin">Yuan Qin</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Kai" sort="Wang, Kai" uniqKey="Wang K" first="Kai" last="Wang">Kai Wang</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Chen, Li Yu" sort="Chen, Li Yu" uniqKey="Chen L" first="Li-Yu" last="Chen">Li-Yu Chen</name><affiliation><nlm:affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Shirley, Neil" sort="Shirley, Neil" uniqKey="Shirley N" first="Neil" last="Shirley">Neil Shirley</name><affiliation><nlm:affiliation>Australian Research Council (ARC) Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus Urrbrae, Adelaide, South Australia, Australia.</nlm:affiliation></affiliation></author><author><name sortKey="Lin, Yann Rong" sort="Lin, Yann Rong" uniqKey="Lin Y" first="Yann-Rong" last="Lin">Yann-Rong Lin</name><affiliation><nlm:affiliation>Department of Agronomy, National Taiwan University, Taipei, Taiwan.</nlm:affiliation></affiliation></author><author><name sortKey="Liu, Li Yu" sort="Liu, Li Yu" uniqKey="Liu L" first="Li-Yu" last="Liu">Li-Yu Liu</name><affiliation><nlm:affiliation>Department of Agronomy, National Taiwan University, Taipei, Taiwan.</nlm:affiliation></affiliation></author><author><name sortKey="Hernandez, Alvaro G" sort="Hernandez, Alvaro G" uniqKey="Hernandez A" first="Alvaro G" last="Hernandez">Alvaro G. Hernandez</name><affiliation><nlm:affiliation>W.M. Keck Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Wright, Chris L" sort="Wright, Chris L" uniqKey="Wright C" first="Chris L" last="Wright">Chris L. Wright</name><affiliation><nlm:affiliation>W.M. Keck Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Bulone, Vincent" sort="Bulone, Vincent" uniqKey="Bulone V" first="Vincent" last="Bulone">Vincent Bulone</name><affiliation><nlm:affiliation>Australian Research Council (ARC) Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus Urrbrae, Adelaide, South Australia, Australia.</nlm:affiliation></affiliation></author><author><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name><affiliation><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Heath, Katy" sort="Heath, Katy" uniqKey="Heath K" first="Katy" last="Heath">Katy Heath</name><affiliation><nlm:affiliation>Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zee, Francis" sort="Zee, Francis" uniqKey="Zee F" first="Francis" last="Zee">Francis Zee</name><affiliation><nlm:affiliation>US Department of Agriculture-Agricultural Research Service (USDA-ARS), Pacific Basin Agricultural Research Center, Hilo, Hawaii, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Moore, Paul H" sort="Moore, Paul H" uniqKey="Moore P" first="Paul H" last="Moore">Paul H. Moore</name><affiliation><nlm:affiliation>Hawaii Agriculture Research Center, Kunia, Hawaii, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Sunkar, Ramanjulu" sort="Sunkar, Ramanjulu" uniqKey="Sunkar R" first="Ramanjulu" last="Sunkar">Ramanjulu Sunkar</name><affiliation><nlm:affiliation>Department of Biochemistry and Molecular Biology, Noble Research Center, Oklahoma State University, Stillwater, Oklahoma, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Leebens Mack, James H" sort="Leebens Mack, James H" uniqKey="Leebens Mack J" first="James H" last="Leebens-Mack">James H. Leebens-Mack</name><affiliation><nlm:affiliation>Department of Plant Biology, University of Georgia, Athens, Georgia, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Mockler, Todd" sort="Mockler, Todd" uniqKey="Mockler T" first="Todd" last="Mockler">Todd Mockler</name><affiliation><nlm:affiliation>Donald Danforth Plant Science Center, St. Louis, Missouri, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Bennetzen, Jeffrey L" sort="Bennetzen, Jeffrey L" uniqKey="Bennetzen J" first="Jeffrey L" last="Bennetzen">Jeffrey L. Bennetzen</name><affiliation><nlm:affiliation>Department of Plant Biology, University of Georgia, Athens, Georgia, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Freeling, Michael" sort="Freeling, Michael" uniqKey="Freeling M" first="Michael" last="Freeling">Michael Freeling</name><affiliation><nlm:affiliation>Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Sankoff, David" sort="Sankoff, David" uniqKey="Sankoff D" first="David" last="Sankoff">David Sankoff</name><affiliation><nlm:affiliation>Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Paterson, Andrew H" sort="Paterson, Andrew H" uniqKey="Paterson A" first="Andrew H" last="Paterson">Andrew H. Paterson</name><affiliation><nlm:affiliation>Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zhu, Xinguang" sort="Zhu, Xinguang" uniqKey="Zhu X" first="Xinguang" last="Zhu">Xinguang Zhu</name><affiliation><nlm:affiliation>Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Gesellschaft Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.</nlm:affiliation></affiliation></author><author><name sortKey="Yang, Xiaohan" sort="Yang, Xiaohan" uniqKey="Yang X" first="Xiaohan" last="Yang">Xiaohan Yang</name><affiliation><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Smith, J Andrew C" sort="Smith, J Andrew C" uniqKey="Smith J" first="J Andrew C" last="Smith">J Andrew C. Smith</name><affiliation><nlm:affiliation>Department of Plant Sciences, University of Oxford, Oxford, UK.</nlm:affiliation></affiliation></author><author><name sortKey="Cushman, John C" sort="Cushman, John C" uniqKey="Cushman J" first="John C" last="Cushman">John C. Cushman</name><affiliation><nlm:affiliation>Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Paull, Robert E" sort="Paull, Robert E" uniqKey="Paull R" first="Robert E" last="Paull">Robert E. Paull</name><affiliation><nlm:affiliation>Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, Hawaii, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Yu, Qingyi" sort="Yu, Qingyi" uniqKey="Yu Q" first="Qingyi" last="Yu">Qingyi Yu</name><affiliation><nlm:affiliation>Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, Texas, USA.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Nature genetics</title><idno type="eISSN">1546-1718</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Ananas (genetics)</term><term>Chromosome Mapping</term><term>Epigenomics</term><term>Evolution, Molecular</term><term>Gene Expression Regulation, Plant</term><term>Gene Regulatory Networks</term><term>Genetic Markers</term><term>Genome, Plant</term><term>Genomics (methods)</term><term>High-Throughput Nucleotide Sequencing (methods)</term><term>Photosynthesis (physiology)</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Genetic Markers</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Ananas</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term><term>High-Throughput Nucleotide Sequencing</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Photosynthesis</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromosome Mapping</term><term>Epigenomics</term><term>Evolution, Molecular</term><term>Gene Expression Regulation, Plant</term><term>Gene Regulatory Networks</term><term>Genome, Plant</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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 gene duplication.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26523774</PMID><DateCreated><Year>2015</Year><Month>12</Month><Day>01</Day></DateCreated><DateCompleted><Year>2016</Year><Month>06</Month><Day>21</Day></DateCompleted><DateRevised><Year>2017</Year><Month>02</Month><Day>20</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1546-1718</ISSN><JournalIssue CitedMedium="Internet"><Volume>47</Volume><Issue>12</Issue><PubDate><Year>2015</Year><Month>Dec</Month></PubDate></JournalIssue><Title>Nature genetics</Title><ISOAbbreviation>Nat. Genet.</ISOAbbreviation></Journal><ArticleTitle>The pineapple genome and the evolution of CAM photosynthesis.</ArticleTitle><Pagination><MedlinePgn>1435-42</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1038/ng.3435</ELocationID><Abstract><AbstractText>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 gene duplication.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ming</LastName><ForeName>Ray</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>VanBuren</LastName><ForeName>Robert</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Donald Danforth Plant Science Center, St. Louis, Missouri, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wai</LastName><ForeName>Ching Man</ForeName><Initials>CM</Initials><AffiliationInfo><Affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tang</LastName><ForeName>Haibao</ForeName><Initials>H</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-3460-8570</Identifier><AffiliationInfo><Affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>iPlant Collaborative/University of Arizona, Tucson, Arizona, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schatz</LastName><ForeName>Michael C</ForeName><Initials>MC</Initials><AffiliationInfo><Affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bowers</LastName><ForeName>John E</ForeName><Initials>JE</Initials><AffiliationInfo><Affiliation>Department of Plant Biology, University of Georgia, Athens, Georgia, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lyons</LastName><ForeName>Eric</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>iPlant Collaborative/University of Arizona, Tucson, Arizona, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Ming-Li</ForeName><Initials>ML</Initials><AffiliationInfo><Affiliation>Hawaii Agriculture Research Center, Kunia, Hawaii, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Jung</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, Hawaii, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Biggers</LastName><ForeName>Eric</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.</Affiliation></AffiliationInfo></Author><Author 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Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Lingmao</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Miao</LastName><ForeName>Wenjing</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Jian</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ye</LastName><ForeName>Zhangyao</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Miao</LastName><ForeName>Chenyong</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Fujian-Taiwan Joint 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Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Guo</LastName><ForeName>Hong</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zheng</LastName><ForeName>Guangyong</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Gesellschaft Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Singh</LastName><ForeName>Ratnesh</ForeName><Initials>R</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-5647-3390</Identifier><AffiliationInfo><Affiliation>Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, Texas, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sharma</LastName><ForeName>Anupma</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, Texas, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Min</LastName><ForeName>Xiangjia</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, Youngstown State University, Youngstown, Ohio, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zheng</LastName><ForeName>Yun</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lee</LastName><ForeName>Hayan</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gurtowski</LastName><ForeName>James</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sedlazeck</LastName><ForeName>Fritz J</ForeName><Initials>FJ</Initials><AffiliationInfo><Affiliation>Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Harkess</LastName><ForeName>Alex</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Plant Biology, University of Georgia, Athens, Georgia, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>McKain</LastName><ForeName>Michael R</ForeName><Initials>MR</Initials><AffiliationInfo><Affiliation>Donald Danforth Plant Science Center, St. Louis, Missouri, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liao</LastName><ForeName>Zhenyang</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fang</LastName><ForeName>Jingping</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Juan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Xiaodan</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Qing</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hu</LastName><ForeName>Weichang</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Qin</LastName><ForeName>Yuan</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Kai</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Li-Yu</ForeName><Initials>LY</Initials><AffiliationInfo><Affiliation>Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign-School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shirley</LastName><ForeName>Neil</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Australian Research Council (ARC) Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus Urrbrae, Adelaide, South Australia, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lin</LastName><ForeName>Yann-Rong</ForeName><Initials>YR</Initials><AffiliationInfo><Affiliation>Department of Agronomy, National Taiwan University, Taipei, Taiwan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Li-Yu</ForeName><Initials>LY</Initials><AffiliationInfo><Affiliation>Department of Agronomy, National Taiwan University, Taipei, Taiwan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hernandez</LastName><ForeName>Alvaro G</ForeName><Initials>AG</Initials><AffiliationInfo><Affiliation>W.M. Keck Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wright</LastName><ForeName>Chris L</ForeName><Initials>CL</Initials><AffiliationInfo><Affiliation>W.M. Keck Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bulone</LastName><ForeName>Vincent</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>Australian Research Council (ARC) Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus Urrbrae, Adelaide, South Australia, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tuskan</LastName><ForeName>Gerald A</ForeName><Initials>GA</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Heath</LastName><ForeName>Katy</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zee</LastName><ForeName>Francis</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>US Department of Agriculture-Agricultural Research Service (USDA-ARS), Pacific Basin Agricultural Research Center, Hilo, Hawaii, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Moore</LastName><ForeName>Paul H</ForeName><Initials>PH</Initials><AffiliationInfo><Affiliation>Hawaii Agriculture Research Center, Kunia, Hawaii, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sunkar</LastName><ForeName>Ramanjulu</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Biochemistry and Molecular Biology, Noble Research Center, Oklahoma State University, Stillwater, Oklahoma, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Leebens-Mack</LastName><ForeName>James H</ForeName><Initials>JH</Initials><AffiliationInfo><Affiliation>Department of Plant Biology, University of Georgia, Athens, Georgia, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mockler</LastName><ForeName>Todd</ForeName><Initials>T</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-0462-5775</Identifier><AffiliationInfo><Affiliation>Donald Danforth Plant Science Center, St. Louis, Missouri, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bennetzen</LastName><ForeName>Jeffrey L</ForeName><Initials>JL</Initials><AffiliationInfo><Affiliation>Department of Plant Biology, University of Georgia, Athens, Georgia, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Freeling</LastName><ForeName>Michael</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sankoff</LastName><ForeName>David</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Paterson</LastName><ForeName>Andrew H</ForeName><Initials>AH</Initials><AffiliationInfo><Affiliation>Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhu</LastName><ForeName>Xinguang</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Gesellschaft Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Xiaohan</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Smith</LastName><ForeName>J Andrew C</ForeName><Initials>JA</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-9188-0258</Identifier><AffiliationInfo><Affiliation>Department of Plant Sciences, University of Oxford, Oxford, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cushman</LastName><ForeName>John C</ForeName><Initials>JC</Initials><AffiliationInfo><Affiliation>Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Paull</LastName><ForeName>Robert E</ForeName><Initials>RE</Initials><AffiliationInfo><Affiliation>Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, Hawaii, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yu</LastName><ForeName>Qingyi</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, Texas, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>R01 HG006677</GrantID><Acronym>HG</Acronym><Agency>NHGRI NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01-HG006677</GrantID><Acronym>HG</Acronym><Agency>NHGRI NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, 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Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D053263" MajorTopicYN="Y">Gene Regulatory Networks</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005819" MajorTopicYN="Y">Genetic Markers</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010788" MajorTopicYN="N">Photosynthesis</DescriptorName><QualifierName UI="Q000502" MajorTopicYN="Y">physiology</QualifierName></MeshHeading></MeshHeadingList><OtherID Source="NLM">NIHMS784544</OtherID><OtherID Source="NLM">PMC4867222</OtherID></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>07</Month><Day>09</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>10</Month><Day>05</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>11</Month><Day>3</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>11</Month><Day>3</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>6</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26523774</ArticleId><ArticleId IdType="pii">ng.3435</ArticleId><ArticleId 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