Hybrid Sequencing in Different Types of Goat Skeletal Muscles Reveals Genes Regulating Muscle Development and Meat Quality
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Animal Management and Sample Collection
2.2. Meat Quality Analysis
2.3. Short-Read RNA Sequencing
2.4. Full-Length RNA Sequencing
2.5. Analysis of Short-Read Sequencing Data
2.6. Analysis of Full-Length Sequencing Raw Data
2.7. Identification and Functional Annotation of Novel Genes and Isoforms
2.8. Identification of lncRNAs and Novel Isoforms’ Open Reading Frames
2.9. Quantitative Real-Time PCR (qPCR) and Data Analysis
3. Results
3.1. Slaughter Performance and Meat Quality
3.2. Transcriptome Profiling of Goat Longissimus Dorsi and Biceps Femoris Muscles
3.3. Characterization of Novel Isoforms
3.4. Alternative Splicing Events Analysis
3.5. Overall Gene Expression Level
3.6. Differentially Expressed Genes and Isoforms in Different Muscles
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Item | Muscle Type | p-Value | |
---|---|---|---|
LD | BF | ||
pH45 min | 6.71 ± 0.13 | 6.94 ± 0.13 | 0.26 |
pH24 h | 5.72 ± 0.06 | 5.83 ± 0.08 | 0.28 |
Lightness, L | 35.35 ± 1.59 | 35.23 ± 1.46 | 0.96 |
Redness, a | 11.63 ± 0.75 b | 14.08 ± 0.41 a | 0.03 |
Yellowness, b | 1.28 ± 0.43 | 0.53 ± 0.37 | 0.23 |
Water loss (%) | 33.02 ± 2.12 | 28.14 ± 5.22 | 0.42 |
Water hold (%) | 48.44 ± 1.98 | 46.33 ± 0.75 | 0.32 |
Shear force (N) | 29.06 ± 2.54 b | 48.65 ± 7.2 a | 0.04 |
Marbling score | 6.00 ± 0.00 a | 5.25 ± 0.25 b | 0.02 |
Type of Reads | Library | ||
---|---|---|---|
1–2 kb | 2–3 kb | 3–6 kb | |
CCS 1 | 144,625 | 133,687 | 135,310 |
5′ reads | 100,807 | 90,964 | 79,482 |
3′ reads | 105,218 | 95,303 | 84,285 |
Poly-A reads | 102,657 | 93,083 | 80,576 |
Filtered short reads | 10,454 | 3043 | 6894 |
Non-full-length reads | 46,175 | 50,806 | 60,436 |
Full-length reads | 87,996 | 79,838 | 67,980 |
FLNC 2 reads | 87,230 | 77,147 | 61,032 |
Average FLNC reads | 1592 | 2604 | 2523 |
Category | Pre-Correction | Post-Correction | Merge |
---|---|---|---|
Unmapped | 2645 (1.17%) | 1159 (0.51%) | 1144 (0.51%) |
Multiple-best | 1467 (0.65%) | 1506 (0.67%) | 1333 (0.59%) |
Low pid | 14,116 (6.26%) | 11,041 (4.90%) | 9935 (4.41%) |
High quality map | 207,181 (91.91%) | 211,703 (93.92%) | 212,997 (94.49%) |
Category | Annotation in RefSeq | Annotation in PacBio Sequences |
---|---|---|
Total Loci | 22,570 | 18,491 |
Loci < 1 K | 4284 (18.98%) | 1214 (6.57%) |
Loci 1–2 K | 5770 (25.56%) | 3254 (17.60%) |
Loci 2–3 K | 4401 (19.50%) | 4637 (25.08%) |
Loci ≥ 3 K | 8115 (35.95%) | 9386 (50.76%) |
Total isoforms | 46,472 | 45,574 |
Gene | BF (Mean FPKM) | LD (Mean FPKM) | log2 (Fold Change) | Enriched Terms |
---|---|---|---|---|
ANKRD1 | 158.10 | 447.93 | 1.49 | 1, 4, 6 |
ANKRD2 | 89.54 | 23.71 | −1.88 | 1, 4, 8, 9 |
PITX1 | 13.10 | 0.48 | −4.76 | 1, 7, 9 |
MYL2 | 11,534.42 | 1795.08 | −2.66 | 2, 6, 10, 11 |
LOC106502520 | 3.71 | 1.10 | −1.88 | 2, 6, 12, 13, 14 |
HOXD9 | 4.94 | 14.39 | 1.56 | 1 |
TPM1 | 8470.62 | 17,679.59 | 1.07 | 3, 6 |
FGF1 | 2.45 | 1.12 | −1.12 | 3 |
FGF9 | 0.93 | 0.18 | −2.38 | 3 |
PROX1 | 4.61 | 1.44 | −1.66 | 5, 6 |
TNNT1 | 7761.57 | 3153.20 | −1.29 | 12, 13 |
LOC102181869 | 4269.46 | 1419.53 | −1.78 | 12, 13, 14 |
WNT5B | 0.92 | 0.33 | −1.45 | 15, 16, 19 |
ADIG | 1.70 | 4.83 | 1.11 | 15, 16, 18, 19 |
LPL | 90.98 | 28.05 | −1.67 | 17, 21 |
LOC106502520 | 3.71 | 1.10 | −1.88 | 22, 23, 24 |
LOC102181869 | 4269.46 | 1419.53 | −1.78 | 22, 23, 24 |
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Pan, Y.; Chen, S.; Niu, S.; Bi, X.; Qiao, L.; Yang, K.; Liu, J.; Liu, W. Hybrid Sequencing in Different Types of Goat Skeletal Muscles Reveals Genes Regulating Muscle Development and Meat Quality. Animals 2021, 11, 2906. https://doi.org/10.3390/ani11102906
Pan Y, Chen S, Niu S, Bi X, Qiao L, Yang K, Liu J, Liu W. Hybrid Sequencing in Different Types of Goat Skeletal Muscles Reveals Genes Regulating Muscle Development and Meat Quality. Animals. 2021; 11(10):2906. https://doi.org/10.3390/ani11102906
Chicago/Turabian StylePan, Yangyang, Sijia Chen, Shu Niu, Xilin Bi, Liying Qiao, Kaijie Yang, Jianhua Liu, and Wenzhong Liu. 2021. "Hybrid Sequencing in Different Types of Goat Skeletal Muscles Reveals Genes Regulating Muscle Development and Meat Quality" Animals 11, no. 10: 2906. https://doi.org/10.3390/ani11102906
APA StylePan, Y., Chen, S., Niu, S., Bi, X., Qiao, L., Yang, K., Liu, J., & Liu, W. (2021). Hybrid Sequencing in Different Types of Goat Skeletal Muscles Reveals Genes Regulating Muscle Development and Meat Quality. Animals, 11(10), 2906. https://doi.org/10.3390/ani11102906