Comparative Transcriptome Analysis of the Skin and the Peritoneal Wall Layer of Triplophysa stenura Distributed in High Elevations
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Fish Samples
2.2. Experimental Methods
2.2.1. Total RNA Extraction
2.2.2. RNA-Seq, De Novo Transcriptome Assembly
2.2.3. Annotation of the Transcriptome and Functional Enrichment Analysis
2.2.4. Gene Expression Level Analysis
2.2.5. Differential Gene Expression Analysis
2.2.6. Validation of Differential Gene Expression by qRT-PCR
3. Results
3.1. Sequencing and Assembly of the T. stenura Transcriptome
3.2. Annotation and Functional Classification
3.3. Screening of DEGs in the Transcriptome in Different Tissues
3.4. GO Annotation of DEGs
3.5. Analysis of KEGG Enrichment Pathway for DEGs
3.6. Screening Candidate Genes Related to the Melanin Synthesis Pathway
3.7. Confirmation of the DEGs Identified with RNA-Seq by Quantitative Real-Time PCR
4. Discussion
4.1. Analysis of DEGs in Different Tissues of T. stenura
4.2. Excavation of the Gene Related to Melanin Synthesis in Different Tissues of T. stenura
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Pathway (C-vs-B) | DEGs with Pathway | q-Value | Pathway ID |
---|---|---|---|
Metabolic pathways | 44 | 2.6501 × 10−23 | ko01100 |
Regulation of actin cytoskeleton | 11 | 4.7186 × 10−14 | ko04810 |
Melanogenesis | 9 | 2.4110 × 10−13 | ko04916 |
Vascular smooth muscle contraction | 11 | 4.8707 × 10−07 | ko04270 |
Wnt signaling pathway | 9 | 4.8710 × 10−07 | ko04310 |
Complement and coagulation cascades | 14 | 1.0766 × 10−06 | ko04610 |
cAMP signaling pathway | 8 | 5.5857 × 10−06 | ko04024 |
Purine metabolism | 5 | 1.3700 × 10−05 | ko00230 |
Rap1 signaling pathway | 14 | 1.3687 × 10−05 | ko04015 |
Calcium signaling pathway | 13 | 1.3687 × 10−05 | ko04020 |
Phospholipase D signaling pathway | 11 | 1.3687 × 10−05 | ko04072 |
Endocytosis | 17 | 1.3687 × 10−05 | ko04144 |
p53 signaling pathway | 6 | 0.00010855 | ko04115 |
PI3K-Akt signaling pathway | 21 | 0.00012699 | ko04151 |
MAPK signaling pathway | 15 | 0.00052534 | ko04010 |
Ras signaling pathway | 12 | 0.00052534 | ko04014 |
RNA transport | 4 | 0.00095378 | ko03013 |
Cell cycle | 5 | 0.00175520 | ko04110 |
Dopaminergic synapse | 8 | 0.00778563 | ko04728 |
Cytokine–cytokine receptor interaction | 10 | 0.01653222 | ko04060 |
Tyrosine metabolism | 1 | 0.02147590 | ko00350 |
Cytokine–cytokine receptor interaction | 10 | 0.02484867 | ko04060 |
Pathway (M-vs-B) | DEGs with Pathway | q-Value | Pathway ID |
---|---|---|---|
Pyrimidine metabolism | 80 | 1.3104 × 10−09 | ko00240 |
Cardiac muscle contraction | 156 | 3.0148 × 10−08 | ko04260 |
MAPK signaling pathway | 312 | 1.3427 × 10−05 | ko04010 |
Ras signaling pathway | 272 | 1.3427 × 10−05 | ko04014 |
Cell cycle | 69 | 2.0339 × 10−05 | ko04110 |
Purine metabolism | 173 | 7.3165 × 10−05 | ko00230 |
Wnt signaling pathway | 123 | 0.00044282 | ko04310 |
Glycolysis/gluconeogenesis | 80 | 0.00045747 | ko00010 |
Cytokine–cytokine receptor interaction | 160 | 0.00087131 | ko04060 |
Rap1 signaling pathway | 280 | 0.00167108 | ko04015 |
Phospholipase D signaling pathway | 251 | 0.00167108 | ko04072 |
PI3K-Akt signaling pathway | 448 | 0.00167108 | ko04151 |
Complement and coagulation cascades | 124 | 0.00167108 | ko04610 |
Tight junction | 274 | 0.00480370 | ko04530 |
Melanogenesis | 84 | 0.00503939 | ko04916 |
Calcium signaling pathway | 285 | 0.00705514 | ko04020 |
cAMP signaling pathway | 276 | 0.00705514 | ko04024 |
p53 signaling pathway | 85 | 0.00976914 | ko04115 |
Ribosome | 98 | 0.01100009 | ko03010 |
Tyrosine metabolism | 38 | 0.01262528 | ko00350 |
DNA replication | 31 | 0.01671852 | ko03030 |
Nucleotide excision repair | 27 | 0.01671852 | ko03420 |
Pathway (M-vs-C) | DEGs with Pathway | q-Value | Pathway ID |
---|---|---|---|
Glycolysis/gluconeogenesis | 86 | 0.027334015 | ko00010 |
Purine metabolism | 173 | 0.01563386 | ko00230 |
Pyrimidine metabolism | 89 | 4.65226 × 10−10 | ko00240 |
Tyrosine metabolism | 31 | 4.73656 × 10−06 | ko00350 |
Glutathione metabolism | 103 | 0.023045646 | ko00480 |
Ribosome | 148 | 0.043198018 | ko03010 |
RNA transport | 63 | 0.015772492 | ko03013 |
DNA replication | 38 | 0.005628575 | ko03030 |
Nucleotide excision repair | 32 | 0.005628575 | ko03420 |
MAPK signaling pathway | 276 | 0.000550616 | ko04010 |
Ras signaling pathway | 254 | 0.000550616 | ko04014 |
Rap1 signaling pathway | 243 | 0.000550616 | ko04015 |
Calcium signaling pathway | 277 | 0.027132289 | ko04020 |
cAMP signaling pathway | 265 | 0.027132289 | ko04024 |
Cytokine–cytokine receptor interaction | 179 | 3.94142 × 10−07 | ko04060 |
Phospholipase D signaling pathway | 229 | 5.24103 × 10−05 | ko04072 |
Cell cycle | 69 | 0.000365611 | ko04110 |
p53 signaling pathway | 89 | 0.027786679 | ko04115 |
PI3K-Akt signaling pathway | 437 | 0.000550616 | ko04151 |
Vascular smooth muscle contraction | 187 | 3.25907 × 10−09 | ko04270 |
Wnt signaling pathway | 102 | 0.029921916 | ko04310 |
Melanogenesis | 74 | 0.008839111 | ko04916 |
Gene ID | Gene Symbol | Description | KEGG Orthology |
---|---|---|---|
Unigene16160_All | asip | agouti signaling protein | K08725 |
Unigene14361_All | adcy2 | adenylate cyclase 2 | K08042 |
Unigene16821_All | adcy9 | adenylate cyclase 9 | K08049 |
CL829.Contig2_All | creb1 | cyclic AMP-responsive element-binding protein 1a | K05870 |
CL1198.Contig1_All | creb3 | cyclic AMP-responsive element-binding protein 3 | K09048 |
Unigene20918_All | wnt2 | wingless-type MMTV integration site family, member 2 | K00182 |
Unigene8674_All | wnt8 | wingless-type MMTV integration site family, member 8 | K00714 |
Unigene10110_All | fzd2 | frizzled 2 | K02375 |
Unigene23239_All | gnao | guanine nucleotide-binding protein G(o) subunit alpha | K04534 |
Unigene7220_All | dvl2 | segment polarity protein dishevelled | K02353 |
Unigene13584_All | gsk3b | glycogen synthase kinase 3 beta | K03083 |
CL1735.Contig2_All | tcf7 | transcription factor 7 | K02620 |
CL5915.Contig5_All | kras | GTPase Kras | K07827 |
Unigene20200_All | hras | GTPase HRas | K02833 |
CL43.Contig11_All | raf1 | RAF-1 proto-oncogene, serine/threonine-protein kinase | K04366 |
Unigene1090_All | map2k1 | mitogen-activated protein kinase kinase 1 | K04368 |
CL2442.Contig2_All | map2k2 | mitogen-activated protein kinase kinase 2 | K04369 |
CL9373.Contig1_All | edn1 | endothelin-1 | K16366 |
CL3664.Contig2_All | gnai | guanine nucleotide-binding protein G(i) subunit alpha | K04630 |
Unigene10095_All | plcb | phosphatidylinositol phospholipase C, beta | K05858 |
Unigene18911_All | calm | calmodulin | K02183 |
CL1057.Contig10_All | camk2 | calcium/calmodulin-dependent protein kinase (CaM kinase) II | K04515 |
Unigene20135_All | prkca | classical protein kinase C alpha type | K02677 |
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Ma, L.; Zhu, Z.; Zhang, S.; Yang, R.; Liu, C.; Yu, Y.; Yang, X. Comparative Transcriptome Analysis of the Skin and the Peritoneal Wall Layer of Triplophysa stenura Distributed in High Elevations. Biology 2024, 13, 5. https://doi.org/10.3390/biology13010005
Ma L, Zhu Z, Zhang S, Yang R, Liu C, Yu Y, Yang X. Comparative Transcriptome Analysis of the Skin and the Peritoneal Wall Layer of Triplophysa stenura Distributed in High Elevations. Biology. 2024; 13(1):5. https://doi.org/10.3390/biology13010005
Chicago/Turabian StyleMa, Li, Zhen Zhu, Shanzhong Zhang, Ruibin Yang, Chen Liu, Yongyao Yu, and Xuefen Yang. 2024. "Comparative Transcriptome Analysis of the Skin and the Peritoneal Wall Layer of Triplophysa stenura Distributed in High Elevations" Biology 13, no. 1: 5. https://doi.org/10.3390/biology13010005
APA StyleMa, L., Zhu, Z., Zhang, S., Yang, R., Liu, C., Yu, Y., & Yang, X. (2024). Comparative Transcriptome Analysis of the Skin and the Peritoneal Wall Layer of Triplophysa stenura Distributed in High Elevations. Biology, 13(1), 5. https://doi.org/10.3390/biology13010005