Based on the Co-Evolution of lncRNAs-Microbiota and Metabolites in Rumen Epithelium to Analyze the Adaptation Characteristics of Tibetan Sheep to Nutrient Stress in the Cold Season
Abstract
:1. Introduction
2. Methods
2.1. Experimental Design and Sample Collection
2.2. Observation of Rumen Epithelial Tissue Morphology and Determination of VFAs, Microbiota, and Metabolites
2.3. Construction of lncRNAs Libraries
2.4. Prediction of LncRNAs
2.5. Identification of DE lncRNAs
2.6. Functional Enrichment of DE lncRNAs
2.7. Prediction of LncRNAs Target Genes
2.8. Construction of lncRNA-mRNA Targeting Network
2.9. RT-qPCR Analysis
2.10. Data Analysis
3. Results
3.1. Overview of Sequencing Data of lncRNAs in Tibetan Sheep Rumen Epithelium Tissue
3.2. Identification and DE lncRNAs in Tibetan Sheep Rumen Epithelium
3.3. Functional Characteristics of DE lncRNAs
3.4. Construction of lncRNA-mRNA Regulatory Network
3.5. The DE lncRNA Was Verified by RT-qPCR
3.6. Association Analysis of lncRNAs with VFAs and Tissue Morphological Characteristics in Rumen Epithelium
3.7. Analysis of lncRNAs-Microbiota-Metabolite Interaction in Rumen Epithelium Tissue
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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LncRNA | Forward (5′ → 3′) | Reverse (5′ → 3′) |
---|---|---|
MSTRG.99282.1 | TGCTTAAACTGGCCCCTCTG | CACCACCGAAAGTCCTCCAA |
MSTRG.118214.1 | GGGCCAGAGACAACTGGAAA | GAATCGTCCAAGGAGACGCA |
MSTRG.89480.2 | GACGAAAGAAAGGCAGCGTC | CCCAGCTGGTTGTTCCTAGAG |
β-actin | AGCCTTCCTTCCTGGGCATGGA | GGACAGCACCGTGTTGGCGTAGA |
Sample | Read Sum | Base Sum | GC (%) | N (%) | Q 20(%) | Q 30(%) |
---|---|---|---|---|---|---|
cold1 | 53,859,439 | 16,025,456,748 | 48.37 | 0 | 98.27 | 94.99 |
cold2 | 60,990,364 | 18,103,396,314 | 48.85 | 0 | 98.34 | 95.04 |
cold3 | 61,090,369 | 18,095,280,638 | 48.28 | 0 | 98.22 | 94.79 |
warm1 | 52,304,300 | 15,558,868,816 | 50.68 | 0 | 98.37 | 95.12 |
warm2 | 54,632,262 | 16,233,111,642 | 51.21 | 0 | 98.38 | 95.17 |
warm3 | 58,382,319 | 17,397,315,876 | 50.83 | 0 | 98.42 | 95.34 |
Sample | Total Reads | Mapped Reads | Uniq Mapped Reads | Multiple Reads |
---|---|---|---|---|
cold1 | 107,718,878 | 93,204,904 (86.53%) | 73,478,583 (68.21%) | 19,726,321 (18.31%) |
cold2 | 121,980,728 | 106,374,890 (87.21%) | 84,457,338 (69.24%) | 21,917,552 (17.97%) |
cold3 | 122,180,738 | 106,430,676 (87.11%) | 82,687,313 (67.68%) | 23,743,363 (19.43%) |
warm1 | 104,608,600 | 73,161,590 (69.94%) | 54,951,260 (52.53%) | 18,210,330 (17.41%) |
warm2 | 109,264,524 | 68,325,730 (62.53%) | 53,242,812 (48.73%) | 15,082,918 (13.80%) |
warm3 | 116,764,638 | 87,757,254 (75.16%) | 69,574,963 (59.59%) | 18,182,291 (15.57%) |
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Liu, X.; Guo, X.; Sha, Y.; He, Y.; Shao, P.; Hu, J.; Wang, J.; Li, S.; Hao, Z. Based on the Co-Evolution of lncRNAs-Microbiota and Metabolites in Rumen Epithelium to Analyze the Adaptation Characteristics of Tibetan Sheep to Nutrient Stress in the Cold Season. Fermentation 2023, 9, 892. https://doi.org/10.3390/fermentation9100892
Liu X, Guo X, Sha Y, He Y, Shao P, Hu J, Wang J, Li S, Hao Z. Based on the Co-Evolution of lncRNAs-Microbiota and Metabolites in Rumen Epithelium to Analyze the Adaptation Characteristics of Tibetan Sheep to Nutrient Stress in the Cold Season. Fermentation. 2023; 9(10):892. https://doi.org/10.3390/fermentation9100892
Chicago/Turabian StyleLiu, Xiu, Xinyu Guo, Yuzhu Sha, Yanyu He, Pengyang Shao, Jiang Hu, Jiqing Wang, Shaobin Li, and Zhiyun Hao. 2023. "Based on the Co-Evolution of lncRNAs-Microbiota and Metabolites in Rumen Epithelium to Analyze the Adaptation Characteristics of Tibetan Sheep to Nutrient Stress in the Cold Season" Fermentation 9, no. 10: 892. https://doi.org/10.3390/fermentation9100892