%0 Journal Article %J Nat Genet %D 2015 %T The pineapple genome and the evolution of CAM photosynthesis. %A Ming, Ray %A VanBuren, Robert %A Wai, Ching Man %A Tang, Haibao %A Schatz, Michael C %A Bowers, John E %A Lyons, Eric %A Wang, Ming-Li %A Chen, Jung %A Biggers, Eric %A Zhang, Jisen %A Huang, Lixian %A Zhang, Lingmao %A Miao, Wenjing %A Zhang, Jian %A Ye, Zhangyao %A Miao, Chenyong %A Lin, Zhicong %A Wang, Hao %A Zhou, Hongye %A Yim, Won C %A Priest, Henry D %A Zheng, Chunfang %A Woodhouse, Margaret %A Edger, Patrick P %A Guyot, Romain %A Guo, Hao-Bo %A Guo, Hong %A Zheng, Guangyong %A Singh, Ratnesh %A Sharma, Anupma %A Min, Xiangjia %A Zheng, Yun %A Lee, Hayan %A Gurtowski, James %A Sedlazeck, Fritz J %A Harkess, Alex %A McKain, Michael R %A Liao, Zhenyang %A Fang, Jingping %A Liu, Juan %A Zhang, Xiaodan %A Zhang, Qing %A Hu, Weichang %A Qin, Yuan %A Wang, Kai %A Chen, Li-Yu %A Shirley, Neil %A Lin, Yann-Rong %A Liu, Li-Yu %A Hernandez, Alvaro G %A Wright, Chris L %A Bulone, Vincent %A Tuskan, Gerald A %A Heath, Katy %A Zee, Francis %A Moore, Paul H %A Sunkar, Ramanjulu %A Leebens-Mack, James H %A Mockler, Todd %A Bennetzen, Jeffrey L %A Freeling, Michael %A Sankoff, David %A Paterson, Andrew H %A Zhu, Xinguang %A Yang, Xiaohan %A Smith, J Andrew C %A Cushman, John C %A Paull, Robert E %A Yu, Qingyi %K Ananas %K Chromosome Mapping %K Epigenomics %K Evolution, Molecular %K Gene Expression Regulation, Plant %K Gene Regulatory Networks %K Genetic Markers %K Genome, Plant %K Genomics %K High-Throughput Nucleotide Sequencing %K Photosynthesis %X

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.

%B Nat Genet %V 47 %P 1435-42 %8 2015 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/26523774?dopt=Abstract %R 10.1038/ng.3435 %0 Journal Article %J Science %D 2012 %T Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. %A Price, Dana C %A Chan, Cheong Xin %A Yoon, Hwan Su %A Yang, Eun Chan %A Qiu, Huan %A Weber, Andreas P M %A Schwacke, Rainer %A Gross, Jeferson %A Blouin, Nicolas A %A Lane, Chris %A Reyes-Prieto, Adrián %A Durnford, Dion G %A Neilson, Jonathan A D %A Lang, B Franz %A Burger, Gertraud %A Steiner, Jürgen M %A Löffelhardt, Wolfgang %A Meuser, Jonathan E %A Posewitz, Matthew C %A Ball, Steven %A Arias, Maria Cecilia %A Henrissat, Bernard %A Coutinho, Pedro M %A Rensing, Stefan A %A Symeonidi, Aikaterini %A Harshavardhan Doddapaneni %A Green, Beverley R %A Rajah, Veeran D %A Boore, Jeffrey %A Bhattacharya, Debashish %K Biological Evolution %K Cyanobacteria %K Cyanophora %K Evolution, Molecular %K Gene Transfer, Horizontal %K Genes, Bacterial %K Genome, Plant %K Molecular Sequence Data %K Photosynthesis %K Phylogeny %K Symbiosis %X

The primary endosymbiotic origin of the plastid in eukaryotes more than 1 billion years ago led to the evolution of algae and plants. We analyzed draft genome and transcriptome data from the basally diverging alga Cyanophora paradoxa and provide evidence for a single origin of the primary plastid in the eukaryote supergroup Plantae. C. paradoxa retains ancestral features of starch biosynthesis, fermentation, and plastid protein translocation common to plants and algae but lacks typical eukaryotic light-harvesting complex proteins. Traces of an ancient link to parasites such as Chlamydiae were found in the genomes of C. paradoxa and other Plantae. Apparently, Chlamydia-like bacteria donated genes that allow export of photosynthate from the plastid and its polymerization into storage polysaccharide in the cytosol.

%B Science %V 335 %P 843-7 %8 2012 Feb 17 %G eng %N 6070 %1 https://www.ncbi.nlm.nih.gov/pubmed/22344442?dopt=Abstract %R 10.1126/science.1213561