Characterization of miRNAs in Embryonic, Larval, and Adult Lumpfish Provides a Reference miRNAome for Cyclopterus lumpus
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Fish Holding
2.2. Ethics Statement
2.3. Sample Collection
2.4. RNA Extraction
2.5. High-Throughput Sequencing (HTS)
2.6. Analysis of Sequencing Data
2.7. Disclosing Putative Differentially Expressed and Organ and Developmental Stage Enriched miRNAs
2.8. RT-qPCR
3. Results
3.1. Total RNA Extraction, Library Preparation, and Small RNA Sequencing
3.2. Characterization of Lumpfish miRNA
3.3. Abundance of miRNAs within Organs and Developmental Stages
3.4. Comparison of Mature miRNA Expression between Organs and Early Developmental Stages
4. Discussion
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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miRNAs | Primer Sequences (5′ to 3′) |
---|---|
clu-miR-25-3p | CATTGCACTTGTCTCGGTCTGA |
clu-miR-17-1-5p | CAAAGTGCTTACAGTGCAGGTA |
clu-miR-122-1-5p | TGGAGTGTGACAATGGTGTTTG |
clu-miR-133ab-3p | TTTGGTCCCCTTCAACCAGCTGT |
clu-miR-205-1-5p | TCCTTCATTCCACCGGAGTCTG |
clu-miR-135c-5p | TATGGCTTTTTATTCCTATGTG |
clu-miR-203-3p | GTGAAATGTTTAGGACCACTTG |
clu-miR-203a-5p | AGTGGTTCTCAACAGTTCAACA |
clu-miR-192a-5p | ATGACCTATGAATTGACAGCCA |
clu-miR-9b-3p | TAAAGCTAGAGAACCGAATGTA |
Organ 1 | miRNAs 2 | Log2FC 3 |
---|---|---|
Brain | clu-miR-31-3p | 6.14 |
Brain | clu-miR-153c-3p | 5.96 |
Brain | clu-miR-153a-3p | 5.33 |
Brain | clu-miR-1788-5p | 4.91 |
Brain | clu-miR-212b-1-5p | 4.10 |
Brain | clu-miR-212b-1-3p | 3.14 |
Brain | clu-miR-128-2-3p | 3.49 |
Brain | clu-miR-338-1-3p | 3.40 |
Brain | clu-miR-132-1-5p | 3.08 |
Muscle | clu-miR-133b-3p | 6.08 |
Muscle | clu-miR-133ab-3p | 5.45 |
Muscle | clu-miR-1-1-3p | 5.23 |
Muscle | clu-miR-1-3-5p | 3.56 |
Gill | clu-miR-31-5p | 6.91 |
Gill | clu-miR-1788-3p | 6.21 |
Gill | clu-miR-203-3p | 5.13 |
Gill | clu-miR-203a-5p | 4.61 |
Gill | clu-miR-375-1-3p | 4.82 |
Gill | clu-miR-205-1-3p | 4.16 |
Gill | clu-miR-200b-3p | 3.8 |
Gill | clu-miR-200b-5p | 3.36 |
Liver | clu-miR-122-1-5p | 8.23 |
Liver | clu-miR-122-1-3p | 7.65 |
Liver | clu-miR-nov3-3p | 6.78 |
Liver | clu-miR-nov3-5p | 4.68 |
Liver | clu-miR-nov1-5p | 5.58 |
Liver | clu-miR-101b-3p | 4.83 |
Liver | clu-miR-101b-5p | 4.41 |
Liver | clu-miR-722-3p | 4.71 |
Liver | clu-miR-722-5p | 4.38 |
Liver | clu-miR-92b-3p | 4.04 |
Liver | clu-miR-92b-5p | 3.91 |
Liver | clu-miR-192a-5p | 3.75 |
Liver | clu-miR-94a-5p | 3.43 |
Liver | clu-miR-152ab-3p | 3.37 |
Liver | clu-miR-nov5-5p | 3.36 |
Spleen | clu-miR-2187b-5p | 5.10 |
Spleen | clu-miR-2187b-3p | 3.47 |
Spleen | clu-miR-460-5p | 3.27 |
Embryos/Larvae 1 | miRNAs 2 | Log2FC 3 |
---|---|---|
Embryos | clu-miR-430b-5-5p | 5.61 |
Embryos | clu-miR-430b-4-3p | 4.51 |
Embryos | clu-miR-430b-1-3p | 4.37 |
Embryos | clu-miR-190b-5p | 5.45 |
Embryos | clu-miR-726-5p | 4.91 |
Embryos | clu-miR-184ab-2-3p | 4.77 |
Embryos | clu-miR-184ab-3p | 4.77 |
Embryos | clu-miR-301b-5p | 4.73 |
Embryos | clu-miR-301b-1-5p | 4.40 |
Embryos | clu-miR-124-1-5p | 4.40 |
Embryos | clu-miR-217b-5p | 4.23 |
Embryos | clu-miR-217a-5p | 4.13 |
Embryos | clu-miR-216a-1-5p | 4.20 |
Larvae | clu-miR-124-1-5p | 4.41 |
Larvae | clu-miR-130-1-5p | 3.15 |
Larvae | clu-miR-130-6-5p | 3.62 |
Larvae | clu-miR-183-5p | 4.09 |
Larvae | clu-miR-184ab-2-3p | 4.71 |
Larvae | clu-miR-184ab-3p | 4.71 |
Larvae | clu-miR-190b-5p | 5.44 |
Larvae | clu-miR-194b-3p | 3.46 |
Larvae | clu-miR-196a-1-5p | 3.95 |
Larvae | clu-miR-216a-1-5p | 4.00 |
Larvae | clu-miR-217a-5p | 4.11 |
Larvae | clu-miR-217b-5p | 4.11 |
Larvae | clu-miR-301b-1-5p | 4.38 |
Larvae | clu-miR-301b-3p | 3.44 |
Larvae | clu-miR-301b-5p | 4.70 |
Larvae | clu-miR-430a-12-3p | 3.97 |
Larvae | clu-miR-430a-3-3p | 3.97 |
Larvae | clu-miR-430b-1-3p | 4.28 |
Larvae | clu-miR-430b-4-3p | 4.40 |
Larvae | clu-miR-430b-5-5p | 5.41 |
Larvae | clu-miR-459-3p | 4.01 |
Larvae | clu-miR-726-5p | 4.64 |
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Chakraborty, S.; Woldemariam, N.T.; Visnovska, T.; Rise, M.L.; Boyce, D.; Santander, J.; Andreassen, R. Characterization of miRNAs in Embryonic, Larval, and Adult Lumpfish Provides a Reference miRNAome for Cyclopterus lumpus. Biology 2022, 11, 130. https://doi.org/10.3390/biology11010130
Chakraborty S, Woldemariam NT, Visnovska T, Rise ML, Boyce D, Santander J, Andreassen R. Characterization of miRNAs in Embryonic, Larval, and Adult Lumpfish Provides a Reference miRNAome for Cyclopterus lumpus. Biology. 2022; 11(1):130. https://doi.org/10.3390/biology11010130
Chicago/Turabian StyleChakraborty, Setu, Nardos T. Woldemariam, Tina Visnovska, Matthew L. Rise, Danny Boyce, Javier Santander, and Rune Andreassen. 2022. "Characterization of miRNAs in Embryonic, Larval, and Adult Lumpfish Provides a Reference miRNAome for Cyclopterus lumpus" Biology 11, no. 1: 130. https://doi.org/10.3390/biology11010130
APA StyleChakraborty, S., Woldemariam, N. T., Visnovska, T., Rise, M. L., Boyce, D., Santander, J., & Andreassen, R. (2022). Characterization of miRNAs in Embryonic, Larval, and Adult Lumpfish Provides a Reference miRNAome for Cyclopterus lumpus. Biology, 11(1), 130. https://doi.org/10.3390/biology11010130