Hepatopancreas Transcriptome Analysis of Spinibarbus sinensis to Reveal Different Growth-Related Genes
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement, Experimental Animals, and Sample Collection
2.2. Date Measurement and Sample Collection
2.3. RNA Isolation, Transcriptome Library Construction, and Sequencing
2.4. Data Processing, Assembly, and Functional Annotation
2.5. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) Enrichment Analysis of DEGs
2.6. Validation of the RNA-seq Analysis by RT-qPCR
2.7. Statistical Analysis
3. Results
3.1. Analysis of Growth Data between FG and SG
3.2. Preliminary Analysis of the Transcriptome Sequences
3.3. DEGs Analysis
3.4. Enrichment and Pathway Analysis of GO and KEGG
3.5. Verification of DEGs with qRT-PCR
4. Discussion
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Gene ID | Annotation | Sequence |
---|---|---|
Cluster-30550.6193 | Serine/Threonine-Protein Kinase 31 (stk 31) | F:AATTGCCAATGATCTATCC R:TCCTCCCACTCAACTCTT |
Cluster-30550.62137 | Probable G-Protein Coupled Receptor 149 (gpr 149) | F:GCATTCGCCACTGCCACTT R:GGTTCGCATCTCCGCTCCT |
Cluster-35286.0 | Angiopoietin-related protein 1 (angptl 1) | F: TGGGAATCACAGACGAGA R: GGAGAAACGAGGCACATA |
Cluster-30550.68321 | Follistatin-related protein 1 (fstl 1) | F: TGGCAGTAATGGGAAGACA R:CGGTCCGTAAGGTAACAAA |
Cluster-30550.18115 | Serine/Threonine-Protein Kinase SIK1 (sik 1) | F: TTCAGGAGGGAAGGAGAT R:ATACGGCTTTGTGGATTG |
Cluster-30550.104720 | Receptor Tyrosine Kinase Like Orphan Receptor 2 (ror 2) | F: ATCTGGCTGCTCGTAACATTCT R:TTGTAGTAGTCGGCTGAGTAGACC |
Cluster-30550.59282 | NLR Family CARD Domain Containing 3 (nlrc 3) | F: CACGCTCTGCCTGTTCTTA R: TCCATTTCCACGCTGTTAT |
Cluster-30550.58994 | PDZ And LIM Domain 2 (pdlim 2) | F:CGGACTCCAACTCCACCT R:GCACGGGATTCTTTGTTC |
Cluster-30550.64357 | Neuron Navigator 2 (nav 2) | F:GTTACCTGGCATCCTCTG R: TCGCTTCCTCCATTTACT |
Cluster-30550.65732 | Bone Morphogenetic Protein 1 (bmp 1) | F:AGAGGAGGCAGAGGACAG R: AAGAGCAGATTGCACCAG |
Cluster-30550.15737 | G-Patch Domain Containing 8 (gpatch 8) | F:CACCGATGATGAGATTGAGA R: GAGAAGAGGGCTGGAGTATG |
Cluster-30550.7707 | Somatostatin 2 (sst 2) | F:AAGGTCAGACAAGCCACA R:CCAAACAGAACAGGGAGA |
Cluster-34620.0 | Kruppel-Like Factor 6 (klf 6) | F:GGTGTTCGTGGGATGGCTGTG R:TGGCTGCATTTGAAAGGTTTGG |
Cluster-36962.2 | Cholecystokinin A Receptor (cckar) | F:TGCTGTAGGGATGATTTG R:CAGTTAGCCTTGTAAGTGTT |
Cluster-30550.43338 | Syncoilin, Intermediate Filament Protein (sync 1) | F: CCCAGATGTTTGAGCATAGCA R:TACCCTTCCTTCTTGGATTTA |
Cluster-30550.53986 | Basic Helix–Loop–Helix Family Member A15 (bhlha 15) | F:AGAGGCGTCTGTGAGGGTG R:AGGCGTTGTTGAGTTTGTG |
Cluster-30550.15279 | Stanniocalcin 1 (stc 1) | F:GAGCCATTCTCGACACTA R: CCCAAGAAGCACTTACAG |
Cluster-34288.0 | S100 Calcium-Binding Protein A1 (s100a1) | F: TGGTATTCCACCGTTATGC R: TCCTCAAAGTTCACCTCCC |
Cluster-30550.58298 | β-actin (β-actin) | F:TTCTTGGGTATGGAGTCTTG R:AGGTCCTTACGGATGTCG |
Sample | Raw Reads | Clean Reads | Clean Bases (%) | Error Rate | Q30 (%) | GC Content (%) |
---|---|---|---|---|---|---|
FG1 | 23,283,837 | 22,964,984 | 6.89 | 0.03 | 94.14 | 45.79 |
FG2 | 22,613,144 | 22,367,822 | 6.71 | 0.03 | 94.03 | 46.32 |
FG3 | 21,152,663 | 20,972,103 | 6.29 | 0.03 | 93.57 | 46.24 |
SG1 | 22,624,801 | 22,377,351 | 6.71 | 0.03 | 94.05 | 46.09 |
SG2 | 23,510,788 | 23,244,189 | 6.97 | 0.03 | 93.89 | 47.18 |
SG3 | 23,310,396 | 23,118,045 | 6.94 | 0.02 | 94.22 | 46.04 |
Assembly statistics (all the clean reads from the 6 libraries were assembled together) | ||||||
Term | Unigene | |||||
N50 | 1635 | |||||
Total Length (bp) | 157,542,467 | |||||
Max Length (bp) | 51,530 | |||||
Min Length (bp) | 301 | |||||
Average Length (bp) | 1050 |
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Zhou, B.; Ling, L.; Wang, B.; Yang, F.; Hou, M.; Liu, F.; Li, Y.; Luo, H.; He, W.; Ye, H. Hepatopancreas Transcriptome Analysis of Spinibarbus sinensis to Reveal Different Growth-Related Genes. Genes 2024, 15, 949. https://doi.org/10.3390/genes15070949
Zhou B, Ling L, Wang B, Yang F, Hou M, Liu F, Li Y, Luo H, He W, Ye H. Hepatopancreas Transcriptome Analysis of Spinibarbus sinensis to Reveal Different Growth-Related Genes. Genes. 2024; 15(7):949. https://doi.org/10.3390/genes15070949
Chicago/Turabian StyleZhou, Bo, Leyan Ling, Bin Wang, Fei Yang, Mengdan Hou, Fan Liu, Yu Li, Hui Luo, Wenping He, and Hua Ye. 2024. "Hepatopancreas Transcriptome Analysis of Spinibarbus sinensis to Reveal Different Growth-Related Genes" Genes 15, no. 7: 949. https://doi.org/10.3390/genes15070949
APA StyleZhou, B., Ling, L., Wang, B., Yang, F., Hou, M., Liu, F., Li, Y., Luo, H., He, W., & Ye, H. (2024). Hepatopancreas Transcriptome Analysis of Spinibarbus sinensis to Reveal Different Growth-Related Genes. Genes, 15(7), 949. https://doi.org/10.3390/genes15070949