Yan Shi1, Xingtan Zhang2, Xiaojun Chang3, Maokai Yan2, Heming Zhao2, Yuan Qin4, Haifeng Wang5,6. 1. State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. 2. Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. 3. College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. 4. Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. yuanqin@fafu.edu.cn. 5. State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. haifengwang@fafu.edu.cn. 6. State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China. haifengwang@fafu.edu.cn.
Abstract
BACKGROUND: Crassulacean acid metabolism (CAM) photosynthesis is an important carbon fixation pathway especially in arid environments because it leads to higher water-use efficiency compared to C3 and C4 plants. However, the role of DNA methylation in regulation CAM photosynthesis is not fully understood. RESULTS: Here, we performed temporal DNA methylome and transcriptome analysis of non-photosynthetic (white base) and photosynthetic (green tip) tissues of pineapple leaf. The DNA methylation patterns and levels in these two tissues were generally similar for the CG and CHG cytosine sequence contexts. However, CHH methylation was reduced in white base leaf tissue compared with green tip tissue across diel time course in both gene and transposon regions. We identified thousands of local differentially methylated regions (DMRs) between green tip and white base at different diel periods. We also showed that thousands of genes that overlapped with DMRs were differentially expressed between white base and green tip leaf tissue across diel time course, including several important CAM pathway-related genes, such as beta-CA, PEPC, PPCK, and MDH. CONCLUSIONS: Together, these detailed DNA methylome and transcriptome maps provide insight into DNA methylation changes and enhance our understanding of the relationships between DNA methylation and CAM photosynthesis.
BACKGROUND:Crassulacean acid metabolism (CAM) photosynthesis is an important carbon fixation pathway especially in arid environments because it leads to higher water-use efficiency compared to C3 and C4 plants. However, the role of DNA methylation in regulation CAM photosynthesis is not fully understood. RESULTS: Here, we performed temporal DNA methylome and transcriptome analysis of non-photosynthetic (white base) and photosynthetic (green tip) tissues of pineapple leaf. The DNA methylation patterns and levels in these two tissues were generally similar for the CG and CHG cytosine sequence contexts. However, CHH methylation was reduced in white base leaf tissue compared with green tip tissue across diel time course in both gene and transposon regions. We identified thousands of local differentially methylated regions (DMRs) between green tip and white base at different diel periods. We also showed that thousands of genes that overlapped with DMRs were differentially expressed between white base and green tip leaf tissue across diel time course, including several important CAM pathway-related genes, such as beta-CA, PEPC, PPCK, and MDH. CONCLUSIONS: Together, these detailed DNA methylome and transcriptome maps provide insight into DNA methylation changes and enhance our understanding of the relationships between DNA methylation and CAM photosynthesis.
Entities:
Keywords:
Ananas comosus; DNA methylation; Epigenetics; Photosynthesis; Transcriptome
Authors: 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 Yu Journal: Nat Genet Date: 2015-11-02 Impact factor: 38.330
Authors: Ching M Wai; Robert VanBuren; Jisen Zhang; Lixian Huang; Wenjing Miao; Patrick P Edger; Won C Yim; Henry D Priest; Blake C Meyers; Todd Mockler; J Andrew C Smith; John C Cushman; Ray Ming Journal: Plant J Date: 2017-08-21 Impact factor: 6.417