Transcriptome and DNA Methylation Analyses of the Molecular Mechanisms Underlying with Longissimus dorsi Muscles at Different Stages of Development in the Polled Yak
Abstract
:1. Introduction
2. Materials and Methods
2.1. Tissue Collection and Library Preparation
2.2. cDNA Library Construction and Sequencing
2.3. RNA-Seq Data Analysis
2.4. Time-series Expression Profile Clustering
2.5. Quantitative PCR Assay
2.6. MethylRAD Library Sequencing
2.7. MethylRAD Data Analysis
3. Results
3.1. Alignment to the Reference Genome
3.2. Differentially Expressed Genes Among the Three Combinations of Groups
3.3. STEM Analysis of DEG Expression Profiles
3.4. KEGG Enrichment Analysis for Time-series Expression Profile Clustering
3.5. qPCR Validation of the Three Developmental Stages of Common DEGs
3.6. Analysis of DNA Methylation and Its Distribution
3.7. Differential Methylation Regions Among the Three Groups
3.8. Enrichment Analysis of DMRs
3.9. Integrated Analysis of DEG and DMP Results
4. Discussion
4.1. KEGG Analysis Based on Time-series Expression Profile Clustering
4.2. Longissimus Dorsi Muscle Methylation Profile and Correlation Analysis of DMR Signaling Pathway
4.3. Negative Correlation Between Methylation Levels of DMPs and Differential Expression of DEGs
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
Abbreviations
References
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Sample | Raw_Reads | Raw_Bases | Clean_Reads | Clean_Bases | Valid_Bases | Q30 1 | GC |
---|---|---|---|---|---|---|---|
E6 | 98.03M | 14.70G | 93.46M | 13.67G | 92.96% | 94.20% | 46.73% |
E7 | 98.27M | 14.74G | 94.05M | 13.77G | 93.45% | 94.57% | 47.06% |
E8 | 99.04M | 14.86G | 93.91M | 13.73G | 92.43% | 93.74% | 47.61% |
M2 | 97.85M | 14.68G | 95.03M | 13.67G | 93.16% | 94.91% | 49.89% |
M3 | 98.12M | 14.72G | 95.08M | 13.78G | 93.64% | 95.01% | 48.90% |
M4 | 99.61M | 14.94G | 96.08M | 13.86G | 92.75% | 94.70% | 51.32% |
A6 | 98.22M | 14.73G | 93.56M | 13.68G | 92.87% | 94.33% | 48.93% |
A7 | 99.56M | 14.93G | 94.64M | 13.86G | 92.83% | 94.00% | 47.78% |
A10 | 99.28M | 14.89G | 94.57M | 13.86G | 93.07% | 94.27% | 48.58% |
Sample | Raw Reads | Enzyme Reads | Mapping Reads | Ratio |
---|---|---|---|---|
E6 | 139,680,224 | 64,643,466 | 30,210,658 | 46.73% |
E7 | 142,659,082 | 65,566,251 | 38,487,733 | 58.70% |
E8 | 142,659,082 | 75,344,977 | 35,403,055 | 46.99% |
M2 | 36,447,959 | 21,083,527 | 9,529,418 | 45.20% |
M3 | 36,447,959 | 22,576,370 | 10,604,071 | 46.97% |
M4 | 36,447,959 | 23,206,057 | 11,126,778 | 47.95% |
A6 | 139,680,224 | 57,187,481 | 30,914,358 | 54.06% |
A7 | 139,680,224 | 65,584,779 | 30,544,305 | 46.57% |
A10 | 139,680,224 | 65,816,098 | 32,854,859 | 49.92% |
Average | 105,931,437 | 51,223,223 | 25,519,471 | 49.23% |
Profile | Profile Number | DMP Group | Two Set Data Overlap Number of DMPs |
---|---|---|---|
profile1_0 | 1811 | A-vs.-E | 274 |
profile1_0 | 1811 | M-vs.-A | 27 |
profile1_0 | 1811 | M-vs.-E | 574 |
profile6 | 3702 | A-vs.-E | 214 |
profile6 | 3702 | M-vs.-A | 18 |
profile6 | 3702 | M-vs.-E | 323 |
Gene | Description | Group |
---|---|---|
IGF2 | insulin-like growth factor 2 | M-E; A-E; profile0_1 |
TMEM8C | transmembrane protein 8c | M-E; A-E; profile0_1 |
MUSTN1 | musculoskeletal, embryonic nuclear protein I | M-E; A-E; profile6 |
CACNA1S | calcium voltage-gated channel subunit alpha1 S | M-E; A-E; profile6 |
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Ma, X.; Jia, C.; Chu, M.; Fu, D.; Lei, Q.; Ding, X.; Wu, X.; Guo, X.; Pei, J.; Bao, P.; et al. Transcriptome and DNA Methylation Analyses of the Molecular Mechanisms Underlying with Longissimus dorsi Muscles at Different Stages of Development in the Polled Yak. Genes 2019, 10, 970. https://doi.org/10.3390/genes10120970
Ma X, Jia C, Chu M, Fu D, Lei Q, Ding X, Wu X, Guo X, Pei J, Bao P, et al. Transcriptome and DNA Methylation Analyses of the Molecular Mechanisms Underlying with Longissimus dorsi Muscles at Different Stages of Development in the Polled Yak. Genes. 2019; 10(12):970. https://doi.org/10.3390/genes10120970
Chicago/Turabian StyleMa, Xiaoming, Congjun Jia, Min Chu, Donghai Fu, Qinhui Lei, Xuezhi Ding, Xiaoyun Wu, Xian Guo, Jie Pei, Pengjia Bao, and et al. 2019. "Transcriptome and DNA Methylation Analyses of the Molecular Mechanisms Underlying with Longissimus dorsi Muscles at Different Stages of Development in the Polled Yak" Genes 10, no. 12: 970. https://doi.org/10.3390/genes10120970
APA StyleMa, X., Jia, C., Chu, M., Fu, D., Lei, Q., Ding, X., Wu, X., Guo, X., Pei, J., Bao, P., Yan, P., & Liang, C. (2019). Transcriptome and DNA Methylation Analyses of the Molecular Mechanisms Underlying with Longissimus dorsi Muscles at Different Stages of Development in the Polled Yak. Genes, 10(12), 970. https://doi.org/10.3390/genes10120970