The pineapple genome and the evolution of CAM photosynthesis.
The pineapple genome and the evolution of CAM photosynthesis.
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DOI：
10.1038/ng.3435
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发表时间：
2015-12
期刊：
影响因子：
30.8
通讯作者：
Yu Q
中科院分区：
文献类型：
--
作者：
Ming R;VanBuren R;Wai CM;Tang H;Schatz MC;Bowers JE;Lyons E;Wang ML;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 WC;Priest HD;Zheng C;Woodhouse M;Edger PP;Guyot R;Guo HB;Guo H;Zheng G;Singh R;Sharma A;Min X;Zheng Y;Lee H;Gurtowski J;Sedlazeck FJ;Harkess A;McKain MR;Liao Z;Fang J;Liu J;Zhang X;Zhang Q;Hu W;Qin Y;Wang K;Chen LY;Shirley N;Lin YR;Liu LY;Hernandez AG;Wright CL;Bulone V;Tuskan GA;Heath K;Zee F;Moore PH;Sunkar R;Leebens-Mack JH;Mockler T;Bennetzen JL;Freeling M;Sankoff D;Paterson AH;Zhu X;Yang X;Smith JA;Cushman JC;Paull RE;Yu Q
菠萝（Ananas comosus（L.）梅尔）是具有高水分利用效率的光合碳同化途径--景天科酸代谢（CAM）的最具经济价值的作物，也是仅次于香蕉的第二重要热带水果。我们对菠萝品种F153和MD 2以及野生菠萝近缘种A. Bracteatus登录号CB 5。菠萝基因组比测序的草基因组少一个古老的全基因组重复，因此，为阐明禾本科现存成员最后共同祖先的基因内容和结构提供了重要参考。菠萝有一个保守的核型与七个前rho重复染色体是祖先现存的草核型。菠萝谱系已经从C3光合作用过渡到CAM，CAM相关基因在光合组织中使用β-碳酸酐酶（βCA）初始捕获CO2，表现出昼夜表达模式。所有三个βCA基因的启动子区都含有一个可以结合昼夜节律核心振荡器的CCA 1结合位点。CAM途径基因富含顺式调控元件，包括与昼夜节律钟基因调控相关的早晨（CCACAC）和晚上（AAAATATC）元件，提供了CAM和昼夜节律钟调控之间的第一个联系。基因相互作用网络分析揭示了激活和抑制的调控元件，控制CAM光合作用的关键酶，表明CAM进化的重构途径预先存在于C3植物。菠萝CAM光合作用是预先存在的基因拷贝的调节性新功能化的结果，而不是通过全基因组或串联基因复制获得新功能化基因。
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 after banana in terms of international trade. We sequenced the genomes of pineapple varieties ‘F153’ and ‘MD2’, and a wild pineapple relative A. bracteatus accession CB5. The pineapple genome has one fewer ancient whole genome duplications than sequenced grass genomes and, therefore, provides an important reference for elucidating gene content and structure in the last common ancestor of extant members of the grass family (Poaceae). Pineapple has a conserved karyotype with seven pre rho duplication chromosomes that are ancestral to extant grass karyotypes. The pineapple lineage has transitioned from C3 photosynthesis to CAM with CAM-related genes exhibiting a diel expression pattern in photosynthetic tissues using beta-carbonic anhydrase (βCA) for initial capture of CO2. Promoter regions of all three βCA genes contain a CCA1 binding site that can bind circadian core oscillators. CAM pathway genes were enriched with cis-regulatory elements including the morning (CCACAC) and evening (AAAATATC) elements associated with regulation of circadian-clock genes, providing the first link between CAM and the circadian clock regulation. Gene-interaction network analysis revealed both activation and repression of regulatory elements that control key enzymes in CAM photosynthesis, indicating that CAM evolved by reconfiguration of pathways preexisting in C3 plants. Pineapple CAM photosynthesis is the result of regulatory neofunctionalization of preexisting gene copies and not acquisition of neofunctionalized genes via whole genome or tandem gene duplication.