Identification and Characterization of Novel circRNAs Involved in Muscle Growth of Blunt Snout Bream (Megalobrama amblycephala)
Abstract
:1. Introduction
2. Results
2.1. Identification of circRNAs and Differential Expression Analysis
2.2. Correlation Analysis between DE circRNAs and Their Source Genes
2.3. Functional Enrichment Analysis of Source Genes and Target miRNAs Prediction
2.4. circRNA–miRNA–mRNA Regulation Networks Construction
2.5. Validation of circRNAs by Quantitative Real Time PCR (qPCR)
3. Discussion
4. Materials and Methods
4.1. Sample Preparation and RNA Extraction
4.2. Library Construction and Whole Transcriptomic Sequencing
4.3. Quality Control
4.4. circRNA Identification
4.5. Differential Expression Analysis
4.6. GO and KEGG Enrichment Analysis
4.7. circRNA–miRNA–mRNA Network Analysis
4.8. Validation of circRNA with qPCR
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Sample | FM1_2 | FM1_3 | FM1_4 | SM1_1 | SM1_2 | SM1_9 |
---|---|---|---|---|---|---|
Raw reads | 115,662,842 | 91,517,836 | 91,790,546 | 84,720,390 | 94,082,116 | 93,420,104 |
Clean reads | 110,866,216 | 88,187,208 | 89,386,380 | 81,888,776 | 89,640,072 | 89,874,446 |
Mapped reads | 99,858,773 | 78,623,397 | 82,180,304 | 72,820,911 | 77,340,146 | 82,612,180 |
Mapping ratio | 90.07% | 89.16% | 91.94% | 88.93% | 86.28% | 91.92% |
Uniquely mapped reads | 91,308,444 | 72,141,305 | 75,688,357 | 67,246,303 | 70,603,603 | 74,848,301 |
Unique mapping ratio | 82.36% | 81.80% | 84.68% | 82.12% | 78.76% | 83.28% |
circRNA ID | Source Gene | FG(TPM) | SG(TPM) | log2(FG/SG) | p-Value |
---|---|---|---|---|---|
novel_circ_0002772 | - | 1619.74 | 0 | 3.17 | 3.09 × 10−5 |
novel_circ_0001521 | dnmt3a | 1048.5 | 0 | 2.75 | 3.93 × 10−4 |
novel_circ_0001576 | txlnb | 795.39 | 0 | 2.41 | 2.11 × 10−3 |
novel_circ_0002295 | vcl | 653.66 | 0 | 2.23 | 4.64 × 10−3 |
novel_circ_0001446 | myom2 | 623.26 | 0 | 2.21 | 5.07 × 10−3 |
novel_circ_0000633 | fam189a2 | 556.98 | 0 | 2.12 | 7.27 × 10−3 |
novel_circ_0001187 | - | 5522.04 | 2070.39 | 1.32 | 8.36 × 10−3 |
novel_circ_0000145 | antxr1 | 524.4 | 0 | 2.07 | 8.78 × 10−3 |
novel_circ_0002879 | pla2g4c | 8396.64 | 605.37 | 2.02 | 9.87 × 10−3 |
novel_circ_0002390 | wdr90 | 453.84 | 0 | 1.91 | 1.58 × 10−2 |
novel_circ_0001407 | cep170 | 449.26 | 0 | 1.9 | 1.59 × 10−2 |
novel_circ_0001464 | nbas | 449.26 | 0 | 1.9 | 1.59 × 10−2 |
novel_circ_0000777 | slc25a21 | 441.98 | 0 | 1.9 | 1.60 × 10−2 |
novel_circ_0000022 | - | 468.1 | 0 | 1.9 | 1.61 × 10−2 |
novel_circ_0000724 | - | 468.1 | 0 | 1.9 | 1.61 × 10−2 |
novel_circ_0002704 | wdr62 | 437.4 | 0 | 1.89 | 1.69 × 10−2 |
novel_circ_0001969 | sik2 | 444.68 | 0 | 1.87 | 1.80 × 10−2 |
novel_circ_0001820 | chchd3 | 434.7 | 0 | 1.87 | 1.81 × 10−2 |
novel_circ_0000213 | - | 406.7 | 0 | 1.81 | 2.16 × 10−2 |
novel_circ_0000748 | ktn1 | 399.41 | 0 | 1.78 | 2.41 × 10−2 |
novel_circ_0002125 | - | 2643.91 | 459.68 | 1.64 | 3.02 × 10−2 |
novel_circ_0002710 | kif1b | 359.56 | 0 | 1.7 | 3.10 × 10−2 |
novel_circ_0000381 | rbpj | 362.26 | 0 | 1.7 | 3.11 × 10−2 |
novel_circ_0002582 | - | 350.4 | 0 | 1.66 | 3.48 × 10−2 |
novel_circ_0002084 | tgm1 | 22909.41 | 4312.85 | 1.59 | 3.58 × 10−2 |
novel_circ_0000560 | efnb1 | 743.67 | 106.89 | 1.58 | 3.89 × 10−2 |
novel_circ_0000761 | dnmt3a | 331.56 | 0 | 1.61 | 4.03 × 10−2 |
novel_circ_0000903 | gtdc1 | 331.56 | 0 | 1.61 | 4.03 × 10−2 |
novel_circ_0001846 | creb3l2 | 326.98 | 0 | 1.6 | 4.08 × 10−2 |
novel_circ_0002104 | - | 2509.35 | 651.04 | 1.46 | 4.10 × 10−2 |
novel_circ_0002034 | yes | 2212.3 | 976.14 | 1.1 | 4.67 × 10−2 |
novel_circ_0002827 | cisd1 | 1134.23 | 291.67 | 1.4 | 4.77 × 10−2 |
novel_circ_0000836 | - | 0 | 627.8 | −2.4 | 2.29 × 10−3 |
novel_circ_0000923 | lmo7 | 1533.34 | 6240.78 | −1.65 | 3.37 × 10−3 |
novel_circ_0001102 | - | 79.72 | 915.02 | −1.99 | 9.54 × 10−3 |
novel_circ_0001684 | grip2 | 229.99 | 1329.04 | −1.76 | 1.07 × 10−2 |
novel_circ_0000919 | lmo7 | 324.28 | 1442.7 | −1.58 | 1.82 × 10−2 |
novel_circ_0001337 | hpse2 | 94.28 | 701.25 | −1.69 | 2.88 × 10−2 |
novel_circ_0001048 | limch1 | 265.27 | 1303.58 | −1.54 | 3.04 × 10−2 |
novel_circ_0002605 | sec24b | 185.56 | 1106.57 | −1.6 | 3.22 × 10−2 |
novel_circ_0001798 | ddx6 | 70.56 | 606.58 | −1.58 | 4.24 × 10−2 |
novel_circ_0001680 | - | 70.56 | 572.13 | −1.56 | 4.46 × 10−2 |
Primer Name | Sequences (5′→3′) | Application |
---|---|---|
circ0002034-F | TACGGGACTGGGATGAGATGA | qPCR |
circ0002034-R | GCCCCTTTAGTGGTCTCACTTT | |
circ0002084-F | TGATGAAGGTTCTGCTGC | |
circ0002084-R | CAACTTCCTCCAGGTCTG | |
circ0002104-F | AAAGCGGATGGATTGGCGTA | |
circ0002104-R | GGGATGAACCTGTCTCCGTG | |
circ0002886-F | ACACCAAGGAAGTATGCAACAGT | |
circ0002886-R | ACAGGGGCCTCCGATATTGT | |
β-actin-F | ACCCACACCGTGCCCATCTA | |
β-actin-R | CGGACAATTTCTCTTTCGGCTG |
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Liu, L.; Chen, Y.; Diao, J.; Luo, L.; Gao, Z. Identification and Characterization of Novel circRNAs Involved in Muscle Growth of Blunt Snout Bream (Megalobrama amblycephala). Int. J. Mol. Sci. 2021, 22, 10056. https://doi.org/10.3390/ijms221810056
Liu L, Chen Y, Diao J, Luo L, Gao Z. Identification and Characterization of Novel circRNAs Involved in Muscle Growth of Blunt Snout Bream (Megalobrama amblycephala). International Journal of Molecular Sciences. 2021; 22(18):10056. https://doi.org/10.3390/ijms221810056
Chicago/Turabian StyleLiu, Lifang, Yulong Chen, Jinghan Diao, Lifei Luo, and Zexia Gao. 2021. "Identification and Characterization of Novel circRNAs Involved in Muscle Growth of Blunt Snout Bream (Megalobrama amblycephala)" International Journal of Molecular Sciences 22, no. 18: 10056. https://doi.org/10.3390/ijms221810056