Identification and Characterization of Extrachromosomal Circular DNA in Slimming Grass Carp
Abstract
:1. Introduction
2. Material and Method
2.1. Samples Collection and DNA Extraction
2.2. Linear DNA Removal and Circular DNA Enrichment
2.3. Illumina Sequencing
2.4. Data Analysis
2.5. Statistical Analysis
3. Results
3.1. Detection of Linear DNA Removal and Circular DNA Enrichment
3.2. The Lansacape of eccDNA
3.3. GC Content Distribution near EccDNA Sequence
3.4. GO Analysis
3.5. Pathway Analysis
3.6. Differential Expression Profile of eccDNAs in Slimming Grass Carp
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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Sample Name | Raw Reads | Clean Reads | Q30 (%) |
---|---|---|---|
Slimming grass carp 1 | 149,672,200 | 130,405,698 | 90.11 |
Slimming grass carp 2 | 185,402,510 | 164,979,168 | 91.25 |
Slimming grass carp 3 | 146,103,008 | 125,514,344 | 89.46 |
Common grass carp 1 | 157,244,712 | 139,871,412 | 91.78 |
Common grass carp 2 | 139,295,000 | 123,377,174 | 91.32 |
Common grass carp 3 | 153,561,782 | 130,942,792 | 91.82 |
Gene Description | Annotation | Regulation | log2FC | p-Value |
---|---|---|---|---|
Muscle fiber structure and development | ||||
Myosin heavy chain, fast skeletal muscle | GC01Gene03301 | Up | 21.2875216485768 | 0.000000051702 |
Myosin light chain, fast skeletal muscle | GC01Gene04413 | Up | 11.7632038868467 | 0.002605161394 |
Myosin binding protein C, fast type a | GC01Gene04318 | Up | 11.7632038868467 | 0.002605161394 |
Myosin, light chain kinase | GC01Gene04351 | Up | 11.7632038868467 | 0.002605161394 |
Myosin phosphatase | GC01Gene04201 | Up | 11.7632038868467 | 0.002605161394 |
Actin, alpha | GC01Gene16235 | Up | 21.2677854176002 | 0.00000005320 |
Capping protein | GC01Gene07223 | Up | 11.2325831506477 | 0.00404054634 |
Muscle segment homeobox C (MsxC) | GC01Gene17144 | Up | 21.0562052584647 | 0.000000072098 |
Integrin | GC01Gene09573 | Down | −9.47427441877102 | 0.00925059453 |
Fibroblast growth factor | GC01Gene14267 | Down | −9.47427441877102 | 0.00925059453 |
Calcium metabolism | ||||
Calsequestrin | GC01Gene12461 | Up | 26.0132467521269 | 0.000000000027 |
Calmodulin | GC01Gene00579 | Up | 21.2677854176002 | 0.00000005320 |
Voltage-sensitive calcium channels | GC01Gene04287 | Up | 11.7632038868467 | 0.002605161394 |
Dihydropyridine (DHP) sensitive calcium channel | GC01Gene04863 | Up | 11.7632038868467 | 0.002605161394 |
Voltage-dependent T-type calcium channel subunit | GC01Gene00457 | UP | 8.55777414188946 | 0.017851975849 |
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He, H.; Gao, Z.; Hu, Z.; Liang, G.; Huang, Y.; Zhou, M.; Liang, R.; Zhang, K. Identification and Characterization of Extrachromosomal Circular DNA in Slimming Grass Carp. Biomolecules 2024, 14, 1045. https://doi.org/10.3390/biom14091045
He H, Gao Z, Hu Z, Liang G, Huang Y, Zhou M, Liang R, Zhang K. Identification and Characterization of Extrachromosomal Circular DNA in Slimming Grass Carp. Biomolecules. 2024; 14(9):1045. https://doi.org/10.3390/biom14091045
Chicago/Turabian StyleHe, Haobin, Zihan Gao, Zehua Hu, Guanyu Liang, Yanhua Huang, Meng Zhou, Rishen Liang, and Kai Zhang. 2024. "Identification and Characterization of Extrachromosomal Circular DNA in Slimming Grass Carp" Biomolecules 14, no. 9: 1045. https://doi.org/10.3390/biom14091045