6mA DNA Methylation on Genes in Plants Is Associated with Gene Complexity, Expression and Duplication
Abstract
:1. Introduction
2. Results
2.1. Genome Assemblies of Four Lotuses
2.2. Patterns of Genome-Wide Distribution of 6mA in Four Lotuses
2.3. The Relationships between 6mA and Gene Expression in Lotus
2.4. Higher Gene Structural Complexity, Expression Level, and Expression Breadth for 6mA-Methylated Genes in Plants
2.5. Evolution of 6mA Modification in Duplicated Genes from Different Origins
2.6. Evolution of 6mA Methylation on Orthologous Genes after Long-Term Species Divergence
3. Discussion
4. Conclusions
5. Materials and Methods
5.1. Plant Materials, Library Construction, and Genome Sequencing
5.2. Genome Assembly and Annotation
5.3. 6mA Modification Detection and Filtering
5.4. Whole-Genome 5mC Analysis
5.5. RNA-seq and Expression Analysis
5.6. Classification of Different Types of Duplicated Genes and Identification of Orthologous Genes
5.7. GO Enrichment Analysis
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Feature | Indian Lotus | Australian Lotus | Russian Lotus | Thai Lotus |
---|---|---|---|---|
Genome size (bp) | 801,742,539 | 807,059,836 | 828,573,050 | 845,764,567 |
Contig number | 421 | 471 | 1608 | 1117 |
Longest contig (bp) | 40,391,228 | 30,603,528 | 14,404,078 | 23,450,770 |
Average contig size (bp) | 1,903,041 | 1,708,757 | 513,269 | 756,434 |
N50 | 9,768,644 | 9,418,673 | 2,477,834 | 4,066,382 |
GC (%) | 38.86 | 38.88 | 38.89 | 38.87 |
BUSCO (%) | 91.8 | 91.6 | 91.1 | 90.9 |
Gene number | 34,966 | 35,093 | 37,129 | 36,314 |
Exon number | 149,316 | 151,500 | 160,545 | 166,936 |
Intron number | 114,350 | 116,407 | 123,416 | 130,622 |
Average CDS length (bp) | 1457.19 | 1458.5 | 1458.81 | 1443.17 |
High-confidence gene (%) | 80.15 | 80.20 | 79.79 | 79.93 |
Repetitive elements (%) | 56.03 | 56.19 | 55.74 | 56.36 |
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Zhang, Y.; Zhang, Q.; Yang, X.; Gu, X.; Chen, J.; Shi, T. 6mA DNA Methylation on Genes in Plants Is Associated with Gene Complexity, Expression and Duplication. Plants 2023, 12, 1949. https://doi.org/10.3390/plants12101949
Zhang Y, Zhang Q, Yang X, Gu X, Chen J, Shi T. 6mA DNA Methylation on Genes in Plants Is Associated with Gene Complexity, Expression and Duplication. Plants. 2023; 12(10):1949. https://doi.org/10.3390/plants12101949
Chicago/Turabian StyleZhang, Yue, Qian Zhang, Xingyu Yang, Xiaofeng Gu, Jinming Chen, and Tao Shi. 2023. "6mA DNA Methylation on Genes in Plants Is Associated with Gene Complexity, Expression and Duplication" Plants 12, no. 10: 1949. https://doi.org/10.3390/plants12101949