Liver Transcriptome Analysis of the Black Porgy (Acanthopagrus schlegelii) under Acute Low-Temperature Stress
Abstract
:1. Introduction
2. Materials and Methods
2.1. Experimental Design and Sample Preparation
2.2. Preparation for RNA-Seq Libraries and Sequencing
2.3. Assembly and Annotation
2.4. Sample Relation Analysis
2.5. Differentially Expressed Genes and Enrichment Analysis
2.6. Validation Using Real-Time Quantitative PCR
3. Results
3.1. Transcriptome Sequencing and Assembly
3.2. Sample Relationship
3.3. Basic Characteristics of Identified Differentially Expressed Genes (DEGs)
3.4. Trend Analysis of Differentially Expressed Genes
3.5. GO and KEGG Enrichment Analysis
3.6. Validation of RNA-Seq Data by qRT-PCR
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Gene Name | Sequence (5′–3′) | Amplification Efficiency/% |
---|---|---|
β-actin | F: CGACGGTCAGGTCATCAC | 91.957 |
R: GCCAGCAGACTCCATTCC | ||
G6PC | F: TACACCGAGACCAAGAAG | 92.611 |
R: GACAGCAGGTAGAAGAGG | ||
GCK | F: GACATCATCTCAAGCACAAG | 94.953 |
R: GGCAACCACATCCATCTC | ||
GPX1 | F: ATCTGCCCTGATGACTGAC | 93.368 |
R: CCTGCTGTAACGCTTGAAG | ||
HSPE1 | F: AGAAGGCTCAAGGCAAAG | 93.504 |
R: TCACGGAACAGGAAATAGTC |
Sample | Rawdata | CleanData (%) | Adapter (%) | LowQuality (%) |
---|---|---|---|---|
AS-1 | 41,124,586 | 99.84 | 0.02 | 0.14 |
AS-2 | 44,151,136 | 99.81 | 0.02 | 0.16 |
AS-3 | 44,722,244 | 99.84 | 0.02 | 0.14 |
AL1-1 | 50,589,846 | 99.78 | 0.03 | 0.19 |
AL1-2 | 44,156,390 | 99.76 | 0.04 | 0.20 |
AL1-3 | 50,278,754 | 99.82 | 0.02 | 0.15 |
AL2-1 | 37,965,772 | 99.85 | 0.02 | 0.13 |
AL2-2 | 38,403,050 | 99.82 | 0.02 | 0.15 |
AL2-3 | 40,782,160 | 99.82 | 0.03 | 0.15 |
Sample | Refer Genes | Sequenced Refer Genes | Average Sequenced Refer Genes | Novel Genes | Sequenced Novel Genes | Average Sequenced Novel Genes | Total Genes | Sequenced Total Genes | Average Sequenced Total Genes |
---|---|---|---|---|---|---|---|---|---|
all | 19,465 | 16,608 | 1064 | 1064 | 20,529 | 17,672 | |||
AS-1 | 19,465 | 13,897 | 14,009 | 1064 | 999 | 1005 | 20,529 | 14,896 | 15,614 |
AS-2 | 19,465 | 14,070 | 1064 | 1011 | 20,529 | 15,081 | |||
AS-3 | 19,465 | 14,060 | 1064 | 1004 | 20,529 | 15,064 | |||
AL1-1 | 19,465 | 13,959 | 13,891 | 1064 | 1005 | 1004 | 20,529 | 14,964 | 14,895 |
AL1-2 | 19,465 | 13,602 | 1064 | 1001 | 20,529 | 14,603 | |||
AL1-3 | 19,465 | 14,113 | 1064 | 1007 | 20,529 | 15,120 | |||
AL2-1 | 19,465 | 13,905 | 14,009 | 1064 | 1003 | 1012 | 20,529 | 14,908 | 15,021 |
AL2-2 | 19,465 | 14,081 | 1064 | 1021 | 20,529 | 15,102 | |||
AL2-3 | 19,465 | 14,041 | 1064 | 1011 | 20,529 | 15,052 |
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Wang, Y.; Chen, Z.; Wei, M.; Lin, Z.; Shen, M.; Zhu, F.; Jia, C.; Meng, Q.; Xu, D.; Du, S.; et al. Liver Transcriptome Analysis of the Black Porgy (Acanthopagrus schlegelii) under Acute Low-Temperature Stress. Life 2023, 13, 721. https://doi.org/10.3390/life13030721
Wang Y, Chen Z, Wei M, Lin Z, Shen M, Zhu F, Jia C, Meng Q, Xu D, Du S, et al. Liver Transcriptome Analysis of the Black Porgy (Acanthopagrus schlegelii) under Acute Low-Temperature Stress. Life. 2023; 13(3):721. https://doi.org/10.3390/life13030721
Chicago/Turabian StyleWang, Yue, Ziqiang Chen, Mingliang Wei, Zhijie Lin, Mingjun Shen, Fei Zhu, Chaofeng Jia, Qian Meng, Dafeng Xu, Shuran Du, and et al. 2023. "Liver Transcriptome Analysis of the Black Porgy (Acanthopagrus schlegelii) under Acute Low-Temperature Stress" Life 13, no. 3: 721. https://doi.org/10.3390/life13030721