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Published on: June 2, 2021
Genome-wide DNA methylation analysis of paulownia with phytoplasma infection
Xibing Cao1, Xiaoqiao Zhai2, Zhenli Zhao1
1Institute of Paulownia, Henan Agricultural University, 95 Wenhua Road, Jinshui District, 450002 Zhengzhou, Henan, PR China; College of Forestry, Henan Agricultural University, 95 Wenhua Road, Jinshui District, 450002 Zhengzhou, PR China.
Abstract:
DNA methylation, an important epigenetic modification, regulates a wide range of biological processes. Previous MSAP results showed that the occurrence of PaWB related to changes of DNA methylation level; however, the relationship between DNA methylation and gene expression remains obscure in paulownia. Therefore, in the present study, we applied WGBS and RNA-seq techniques to investigate the DNA methylation and gene expression changes between healthy Paulownia fortunei seedlings and the phytoplasma-infected ones. A map of methylated cytosines at the single base pair resolution of paulownia was constructed. Compared to the healthy seedlings, the DNA methylation level increased after phytoplasma infection, and the change of mCHH was the main methylation pattern. DMR analysis showed that 422,662 DMRs in the genome were identified, in which, 27,871 DMR-associated genes were differentially expressed. Finally, 436 genes with significant differences in their methylation levels and mRNA expression profiles were identified through integrated analysis of the DNA methylomic and transcriptomic. KEGG pathway analysis revealed that these genes are mainly involved in plant hormone signal transduction, carbon metabolism, and starch and sucrose metabolism pathways. Two of DMR-associated genes were verified by BS- PCR. Finally, we selected TRP 1 and R2R3-MYB protein were closely related to the occurrence of PaWB. Our findings provide valuable insight into the mechanism of PaWB at the epigenetic level.
Insights
Phytoplasma infection in Paulownia fortunei increases DNA methylation, altering gene expression. This epigenetic shift impacts pathways like hormone signaling and metabolism, revealing key genes like TRP 1 and R2R3-MYB involved in PaWB.
Area of Science:
- Plant Science
- Epigenetics
- Molecular Biology
Background:
- DNA methylation is a crucial epigenetic modification regulating biological processes.
- Previous studies suggested a link between DNA methylation changes and Paulownia witches' broom (PaWB).
- The precise relationship between DNA methylation and gene expression in Paulownia remains unclear.
Purpose of the Study:
- To investigate DNA methylation and gene expression changes in Paulownia fortunei seedlings upon phytoplasma infection.
- To construct a single base pair resolution map of methylated cytosines in Paulownia.
- To elucidate the epigenetic mechanisms underlying PaWB.
Main Methods:
- Whole Genome Bisulfite Sequencing (WGBS) to map DNA methylation.
- RNA sequencing (RNA-seq) to analyze gene expression.
- Differential Methylation Region (DMR) analysis and integrated methylomic-transcriptomic analysis.
Main Results:
- DNA methylation levels increased in phytoplasma-infected seedlings, with mCHH being the predominant pattern.
- 422,662 DMRs were identified, with 27,871 DMR-associated genes showing differential expression.
- 436 genes exhibited significant changes in both methylation and mRNA expression, primarily involved in hormone signaling and carbohydrate metabolism.
Conclusions:
- Phytoplasma infection induces significant DNA methylation alterations in Paulownia.
- Integrated analysis identified key genes, including TRP 1 and R2R3-MYB, associated with PaWB occurrence.
- These findings offer insights into the epigenetic regulation of PaWB.
