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DNA甲基化组和转录组的综合分析揭示了菠萝中景天酸代谢光合作用的表观遗传调控。

Integrated analysis of DNA methylome and transcriptome reveals epigenetic regulation of CAM photosynthesis in pineapple.

作者信息

Shi Yan, Zhang Xingtan, Chang Xiaojun, Yan Maokai, Zhao Heming, Qin Yuan, Wang Haifeng

机构信息

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.

Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.

出版信息

BMC Plant Biol. 2021 Jan 6;21(1):19. doi: 10.1186/s12870-020-02814-5.

DOI:10.1186/s12870-020-02814-5
PMID:33407144
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7789485/
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.

摘要

背景

景天酸代谢（CAM）光合作用是一种重要的碳固定途径，尤其在干旱环境中，因为与C3和C4植物相比，它具有更高的水分利用效率。然而，DNA甲基化在调节CAM光合作用中的作用尚未完全了解。

结果

在这里，我们对菠萝叶的非光合（白色基部）和光合（绿色叶尖）组织进行了时间DNA甲基化组和转录组分析。在CG和CHG胞嘧啶序列背景下，这两种组织中的DNA甲基化模式和水平总体相似。然而，在基因和转座子区域的整个昼夜时间进程中，白色基部叶片组织中的CHH甲基化与绿色叶尖组织相比有所降低。我们在不同的昼夜时段鉴定出绿色叶尖和白色基部之间数千个局部差异甲基化区域（DMR）。我们还表明，在整个昼夜时间进程中，数千个与DMR重叠的基因在白色基部和绿色叶尖叶片组织之间差异表达，包括几个重要的CAM途径相关基因，如β - CA、PEPC、PPCK和MDH。

结论

总之，这些详细的DNA甲基化组和转录组图谱为DNA甲基化变化提供了见解，并增强了我们对DNA甲基化与CAM光合作用之间关系的理解。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c511/7789485/0985ace10025/12870_2020_2814_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c511/7789485/ce512168510b/12870_2020_2814_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c511/7789485/04dbe8ede6e4/12870_2020_2814_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c511/7789485/e9fa6f5daa77/12870_2020_2814_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c511/7789485/6f1d7756d4b8/12870_2020_2814_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c511/7789485/49fd4ec2525b/12870_2020_2814_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c511/7789485/0985ace10025/12870_2020_2814_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c511/7789485/ce512168510b/12870_2020_2814_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c511/7789485/04dbe8ede6e4/12870_2020_2814_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c511/7789485/e9fa6f5daa77/12870_2020_2814_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c511/7789485/6f1d7756d4b8/12870_2020_2814_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c511/7789485/49fd4ec2525b/12870_2020_2814_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c511/7789485/0985ace10025/12870_2020_2814_Fig6_HTML.jpg

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