A First Insight into the Gonad Transcriptome of Hong Kong Catfish (Clarias fuscus)
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Sample Collection and RNA Extraction
2.3. Full-Length Transcriptome Sequencing
2.4. Illumina Transcriptome Sequencing
2.5. Transcriptome Gene Annotation
2.6. Identification of lncRNAs and Simple Sequence Repeats (SSRs)
2.7. Differential Expression Gene Analysis
2.8. Gene Expression Validation
3. Results
3.1. Transcriptome Data from the Gonads of Hong Kong Catfish
3.2. Transcriptome Annotation
3.3. Identification of lncRNAs and SSRs
3.4. Identification of Sex-Biased Genes and Enrichment Analysis
3.5. Validation of RNA-seq Results by qRT-PCR
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Conflicts of Interest
References
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Item | Full-Length Transcriptome |
---|---|
Number of CCS | 290,291 |
Read bases of CCS | 727,649,017 |
Average read length of CCS | 2506 |
Number of FLNC reads | 248,408 |
Number of consensus isoforms | 69,148 |
Number of high-quality isoforms | 66,958 |
Number of unigenes | 37,305 |
Group | Clean Read Number | Clean Base Number | Q30 (%) | Q20 (%) | GC Content (%) | Mapping Rate (%) |
---|---|---|---|---|---|---|
Female1 | 23,589,409 | 7,063,060,762 | 95.02 | 98.27 | 50.11 | 88.30 |
Female2 | 26,686,421 | 7,990,222,868 | 95.01 | 98.28 | 49.97 | 87.40 |
Female3 | 23,801,164 | 7,125,984,844 | 95.15 | 98.34 | 49.94 | 88.13 |
Male1 | 21,172,626 | 6,329,873,382 | 94.36 | 97.82 | 48.59 | 74.74 |
Male2 | 25,166,743 | 7,532,229,636 | 94.29 | 97.82 | 48.54 | 75.58 |
Male3 | 24,181,267 | 7,231,220,526 | 94.66 | 97.97 | 48.14 | 74.17 |
Annotation Database | Number of Unigenes |
---|---|
GO annotation | 26,710 |
KEGG annotation | 22,010 |
KOG annotation | 25,866 |
Pfam annotation | 29,797 |
Swissprot annotation | 34,144 |
eggNOG annotation | 33,442 |
NR annotation | 34,221 |
All annotated | 34,342 |
Pathway ID | Pathway Term | p-Value |
---|---|---|
ko03010 | Ribosome | 1.20 × 10−14 |
ko03460 | Fanconi anemia pathway | 0.001289 |
ko00061 | Fatty acid biosynthesis | 0.002237 |
ko04110 | Cell cycle | 0.002476 |
ko04512 | ECM-receptor interaction | 0.003232 |
ko00900 | Terpenoid backbone biosynthesis | 0.004637 |
ko03030 | DNA replication | 0.008156 |
ko00062 | Fatty acid elongation | 0.008802 |
ko00230 | Purine metabolism | 0.010252 |
ko00130 | Ubiquinone and other terpenoid-quinone biosynthesis | 0.010259 |
ko01212 | Fatty acid metabolism | 0.014225 |
ko00670 | One carbon pool by folate | 0.018081 |
ko00604 | Glycosphingolipid biosynthesis—ganglio series | 0.027686 |
ko00910 | Nitrogen metabolism | 0.030108 |
ko04270 | Vascular smooth muscle contraction | 0.044731 |
ko00600 | Sphingolipid metabolism | 0.049852 |
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Lin, X.; Zhou, D.; Zhang, X.; Li, G.; Zhang, Y.; Huang, C.; Zhang, Z.; Tian, C. A First Insight into the Gonad Transcriptome of Hong Kong Catfish (Clarias fuscus). Animals 2021, 11, 1131. https://doi.org/10.3390/ani11041131
Lin X, Zhou D, Zhang X, Li G, Zhang Y, Huang C, Zhang Z, Tian C. A First Insight into the Gonad Transcriptome of Hong Kong Catfish (Clarias fuscus). Animals. 2021; 11(4):1131. https://doi.org/10.3390/ani11041131
Chicago/Turabian StyleLin, Xinghua, Dayan Zhou, Xiaomin Zhang, Guangli Li, Yulei Zhang, Cailin Huang, Zhixin Zhang, and Changxu Tian. 2021. "A First Insight into the Gonad Transcriptome of Hong Kong Catfish (Clarias fuscus)" Animals 11, no. 4: 1131. https://doi.org/10.3390/ani11041131
APA StyleLin, X., Zhou, D., Zhang, X., Li, G., Zhang, Y., Huang, C., Zhang, Z., & Tian, C. (2021). A First Insight into the Gonad Transcriptome of Hong Kong Catfish (Clarias fuscus). Animals, 11(4), 1131. https://doi.org/10.3390/ani11041131