Characterization and Comparative Transcriptomic Analysis of Skeletal Muscle in Pekin Duck at Different Growth Stages Using RNA-Seq
Abstract
:Simple Summary
Abstract
1. Introduction
2. Material and Methods
2.1. Ethics Approval and Consent to Participate
2.2. Animal and Tissue Collection
2.3. RNA Isolation, Library Preparation and Sequencing
2.4. Quality Control and Comparative Analysis
2.5. SNP/InDel Analysis and Prediction of AS
2.6. New Genes Analysis
2.7. Quantification and Differential Expression Analysis
2.8. Analysis of GO Enrichment and KEGG Pathway Enrichment
2.9. Protein–Protein Interaction Network
2.10. Verification of Results by qPCR
3. Results
3.1. Evaluation of Transcriptome Profiles
3.2. Annotation and Classification of SNP/InDel
3.3. Prediction of Alternative Splicing
3.4. New Genes Analysis
3.5. Gene Functional Annotation and Classification
3.6. Analysis of Differentially Expressed Genes
3.7. GO Annotation and KEGG Pathway Analysis
3.8. Analysis of Protein–Protein Interaction Network
3.9. Validation of RNA-Seq Results
4. Discussion
4.1. Analysis Summary of Sequencing Data
4.2. Annotation and Classification of SNP/InDel in Skeletal Muscle Developmental Process
4.3. Alternative Splicing Events in Skeletal Muscle Developmental Process
4.4. DEGs Analyzed at All Time Points
4.5. Analysis of GO and KEGG Pathway
4.6. Analysis of Protein–Protein Interaction Network
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Groups | Primer Name | Primer Sequence (5′-3′) | Size | Regulated |
---|---|---|---|---|
β-actin | F: CCCTGTATGCCTCTGGTCG | 194 bp | ||
R: CTCGGCTGTGGTGGTGAAG | ||||
GAPDH | F: CTGGTGCTGAATACGTTGTGG | 198 bp | ||
R: CTGGTGCTGAATACGTTGTGG | ||||
PE17B_vs_ PE21B | HOXC8 | F:ACTACTGCTCCCACCTTCCA | 168 bp | DOWN |
R:AAGCGATTGCCTCGGTAGAG | ||||
KLHL31 | F: AACCAGTGCGTGACAGTGAT | 171 bp | UP | |
R: GCTGAAGTGGGTACGCTTCT | ||||
PE21B_vs_ PE27B | DUSP10 | F:GGCAAGATCACCGTCTTGGA | 173 bp | UP |
R:TCCTTGCCTTCTCGCTTGAG | ||||
FBXO32 | F: GTCGGCAAATCTGTCCTGGT | 196 bp | UP | |
R: GGCTAACCAGGTCTCTCCCA | ||||
PE27B_vs_ PM6B | ADGRL3 | F:CCAATGCTCTGCTTCGTCCT | 143 bp | DOWN |
R:GGCATTGTTCAGAAGCCCCT | ||||
POSTN | F: GCAGGGAGCTGGAACTGAG | 148 bp | DOWN | |
R: TGTTGCTCCTCCTTGTGTCC | ||||
PE17L_vs_ PE21L | MFRP | F:AGTTCTGCAACCCCGTCTTC | 151 bp | DOWN |
R:CAGGTGAACCTACAGTCGGC | ||||
GPR37 | F: CGCCAGTCCTCCTTTTCTGT | 175 bp | DOWN | |
R: ATTTCACGACGGATGGTGCT | ||||
PE21L_vs_ PE27L | PCSK2 | F:TGTAGCTGAAGCATGGGAGC | 128 bp | UP |
R:TGAAGTCGTAGCTGGCTTGG | ||||
MYL4 | F:CCTGACCCCAAAAAGGATGC | 116 bp | DOWN | |
R:AACTCTTCGATCTGCTCGGC | ||||
PE27L_vs_ PM6L | TDP1 | F:GCTTGGTTCTACCCCTGGAC | 132 bp | DOWN |
R:AACTGTCCAACAACAGGCCA | ||||
AXIN2 | F: GCTACCAAGACCTACATAAG | 222 bp | DOWN | |
R: GAGATAGCCACAGACAACT |
Samples | Clean Reads | Clean Bases | GC Content | Q30 Value |
---|---|---|---|---|
PE17B1 | 21,975,680 | 6,554,209,528 | 51.62% | 93.01% |
PE17B2 | 24,902,534 | 7,429,488,988 | 50.72% | 92.96% |
PE17B3 | 27,675,557 | 8,261,513,254 | 51.50% | 93.12% |
PE17L1 | 29,364,381 | 8,772,703,244 | 51.20% | 92.69% |
PE17L2 | 31,153,547 | 9,309,596,992 | 51.11% | 93.22% |
PE17L3 | 24,302,063 | 7,263,420,576 | 50.37% | 92.66% |
PE21B1 | 22,936,235 | 6,848,636,870 | 51.28% | 92.96% |
PE21B2 | 25,545,188 | 7,617,899,452 | 51.47% | 92.59% |
PE21B3 | 23,616,893 | 7,047,370,582 | 50.76% | 93.11% |
PE21L1 | 23,419,211 | 7,007,727,954 | 51.72% | 93.02% |
PE21L2 | 21,134,566 | 6,316,620,646 | 51.41% | 93.05% |
PE21L3 | 25,503,895 | 7,612,558,182 | 51.26% | 93.11% |
PE27B1 | 23,860,738 | 7,133,252,550 | 50.70% | 92.86% |
PE27B2 | 23,257,098 | 6,947,415,186 | 50.96% | 92.74% |
PE27B3 | 21,883,412 | 6,534,290,346 | 51.66% | 92.93% |
PE27L1 | 24,872,668 | 7,420,346,180 | 51.81% | 92.88% |
PE27L2 | 23,784,499 | 7,108,311,764 | 51.94% | 92.91% |
PE27L3 | 27,447,436 | 8,197,076,086 | 51.74% | 92.71% |
PM6B1 | 27,026,755 | 8,072,713,512 | 53.75% | 92.78% |
PM6B2 | 24,555,447 | 7,338,843,490 | 53.63% | 92.87% |
PM6B3 | 22,180,858 | 6,629,939,152 | 54.51% | 93.24% |
PM6L1 | 27,342,141 | 8,173,286,426 | 53.45% | 93.48% |
PM6L2 | 25,702,190 | 7,668,643,964 | 53.48% | 93.34% |
PM6L3 | 21,228,238 | 6,343,509,968 | 53.24% | 92.93% |
Samples | AS Number | Samples | AS Number |
---|---|---|---|
PE17B1 | 42,619 | PE17L1 | 45,818 |
PE17B2 | 43,505 | PE17L2 | 47,889 |
PE17B3 | 45,395 | PE17L3 | 47,567 |
PE21B1 | 41,937 | PE21L1 | 36,118 |
PE21B2 | 42,880 | PE21L2 | 39,346 |
PE21B3 | 43,413 | PE21L3 | 44,668 |
PE27B1 | 43,374 | PE27L1 | 36,949 |
PE27B2 | 45,707 | PE27L2 | 35,841 |
PE27B3 | 38,412 | PE27L3 | 37,077 |
PM6B1 | 40,585 | PM6L1 | 39,332 |
PM6B2 | 35,912 | PM6L2 | 38,184 |
PM6B3 | 32,256 | PM6L3 | 36,346 |
Annotated Databases | New Gene Number |
---|---|
COG | 26 |
GO | 97 |
KEGG | 55 |
KOG | 77 |
Pfam | 68 |
Swiss-Prot | 55 |
eggNOG | 154 |
Nr | 297 |
All | 299 |
DEG Set | Total | COG | GO | KEGG | KOG | NR | Pfam | Swiss-Prot | eggNOG |
---|---|---|---|---|---|---|---|---|---|
PE17B_vs_ PE21B | 358 | 123 | 279 | 225 | 247 | 357 | 324 | 263 | 344 |
PE21B_vs_ PE27B | 1511 | 495 | 1206 | 1021 | 1070 | 1503 | 1354 | 1090 | 1446 |
PE27B_vs_ PM6B | 3643 | 1289 | 2924 | 2448 | 2656 | 3630 | 3342 | 2635 | 3519 |
PE17L_vs_ PE21L | 624 | 238 | 492 | 417 | 443 | 621 | 561 | 463 | 598 |
PE21L_vs_ PE27L | 274 | 82 | 207 | 171 | 167 | 274 | 233 | 186 | 258 |
PE27L_vs_ PM6L | 2323 | 841 | 1896 | 1614 | 1691 | 2316 | 2152 | 1744 | 2265 |
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Hu, Z.; Cao, J.; Ge, L.; Zhang, J.; Zhang, H.; Liu, X. Characterization and Comparative Transcriptomic Analysis of Skeletal Muscle in Pekin Duck at Different Growth Stages Using RNA-Seq. Animals 2021, 11, 834. https://doi.org/10.3390/ani11030834
Hu Z, Cao J, Ge L, Zhang J, Zhang H, Liu X. Characterization and Comparative Transcriptomic Analysis of Skeletal Muscle in Pekin Duck at Different Growth Stages Using RNA-Seq. Animals. 2021; 11(3):834. https://doi.org/10.3390/ani11030834
Chicago/Turabian StyleHu, Zhigang, Junting Cao, Liyan Ge, Jianqin Zhang, Huilin Zhang, and Xiaolin Liu. 2021. "Characterization and Comparative Transcriptomic Analysis of Skeletal Muscle in Pekin Duck at Different Growth Stages Using RNA-Seq" Animals 11, no. 3: 834. https://doi.org/10.3390/ani11030834
APA StyleHu, Z., Cao, J., Ge, L., Zhang, J., Zhang, H., & Liu, X. (2021). Characterization and Comparative Transcriptomic Analysis of Skeletal Muscle in Pekin Duck at Different Growth Stages Using RNA-Seq. Animals, 11(3), 834. https://doi.org/10.3390/ani11030834