Combined Profiling of Transcriptome and DNA Methylome Reveal Genes Involved in Accumulation of Soluble Sugars and Organic Acid in Apple Fruits
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials and Treatment
2.2. Measurement of Organic Acid and Soluble Sugar Contents
2.3. Bisulfite Sequencing (BS) Library Construction and Data Analysis
2.4. RNA Sequencing (RNA-Seq) and Identification of Differentially Expressed Genes (DEGs)
2.5. Subcellular Localization of MdTSTa and MdMa11 in N. benthamiana Leaf Epidermal Cells
2.6. Functional Analysis of MdTSTa and MdMa11
3. Results
3.1. Phenotypic Difference between ‘HC’ and ‘QG’ Mature Apple Fruits
3.2. Genome-Wide Methylation Profiles in ‘HC’ and ‘QG’ Mature Fruits
3.3. Distribution of DNA Methylation among Gene Features and TEs
3.4. Identification and Analyses of the Distribution and Functions of the Differentially Methylated Regions (DMRs) between ‘HC’ and ‘QG’ Mature Fruits
3.5. Analysis of the Association between the Transcriptome and DNA Methylation
3.6. Differences in the Expression and Methylation Levels of Genes Involved in Soluble Sugar and Organic Acid Metabolism between ‘HC’ and ‘QG’ Mature Fruits
3.7. Vacuolar Transporter Genes: Differences in the Expression and Methylation Levels between ‘HC’ and ‘QG’ Mature Fruits
3.8. Identification and Functional Analysis of Genes Involved in Soluble Sugar Accumulation
3.9. Identification of a Candidate Gene Affecting Vacuolar Acidity
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Ma, W.; Li, B.; Zheng, L.; Peng, Y.; Tian, R.; Yuan, Y.; Zhu, L.; Su, J.; Ma, F.; Li, M.; et al. Combined Profiling of Transcriptome and DNA Methylome Reveal Genes Involved in Accumulation of Soluble Sugars and Organic Acid in Apple Fruits. Foods 2021, 10, 2198. https://doi.org/10.3390/foods10092198
Ma W, Li B, Zheng L, Peng Y, Tian R, Yuan Y, Zhu L, Su J, Ma F, Li M, et al. Combined Profiling of Transcriptome and DNA Methylome Reveal Genes Involved in Accumulation of Soluble Sugars and Organic Acid in Apple Fruits. Foods. 2021; 10(9):2198. https://doi.org/10.3390/foods10092198
Chicago/Turabian StyleMa, Wenfang, Baiyun Li, Litong Zheng, Yunjing Peng, Rui Tian, Yangyang Yuan, Lingcheng Zhu, Jing Su, Fengwang Ma, Mingjun Li, and et al. 2021. "Combined Profiling of Transcriptome and DNA Methylome Reveal Genes Involved in Accumulation of Soluble Sugars and Organic Acid in Apple Fruits" Foods 10, no. 9: 2198. https://doi.org/10.3390/foods10092198