Full-Length Transcriptome Reconstruction Reveals the Genetic Mechanisms of Eyestalk Displacement and Its Potential Implications on the Interspecific Hybrid Crab (Scylla serrata ♀ × S. paramamosain ♂)
Abstract
:Simple Summary
Abstract
1. Introduction
2. Material and Methods
2.1. Sample Collection, RNA Extraction and Sequencing
2.2. SMRT Sequencing Data Processing
2.3. Collapsing Redundant Transcripts Isoforms
2.4. Completeness and Characteristics Analysis of Reconstructed Transcriptomes
2.5. Gene Functional Annotation
2.6. Alternative Splicing (AS) Events Analysis
2.7. Quantification of Identified Transcripts
2.8. Differential Alternative Splicing (DAS) Events, Differential Expressed Transcripts (DETs), and Their Enrichment Analysis
2.9. Validation of AS Events and Differential Expressed Genes
3. Results
3.1. Summary of PacBio Iso-Seq Data
3.2. Collapsing Redundant Isoforms
3.3. Evaluation of Reconstructed Transcriptomes
3.4. Functional Annotation
3.5. Alternative Splicing (AS) Events
3.6. Differential Alternative Splicing (DAS) Events, Differential Expressed Transcripts (DETs), and Their Enrichment Analysis
3.7. Validation of Alternative Splicing (AS) Events and Significant Differential Expression Transcripts (DGEs)
4. Discussions
4.1. Reconstructed Transcriptomes Based on the Non-Hybrid Correction Methods and Two-Step Collapsing Strategy
4.2. The Genetic Mechanisms of Eyestalk Displacement and Its Potential Implications on the Novel Interspecific Hybrid Crab
4.3. The Transcriptomes Difference between Purebred (SPA) and Crossbred (NH and DH) Mud Crabs
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Sample | Types | Numbers of Sequences | Length of Isoforms | N50 9 | ||
---|---|---|---|---|---|---|
Min | Mean | Max | ||||
SPA 1 | Subreads | 12,705,473 | 51 | 1636.8 | 211,052 | 1962 |
CCS 4 | 265,745 | 104 | 1904 | 14,128 | 2177 | |
FL 5 | 226,748 | 99 | 1814.2 | 10,492 | 2109 | |
FLCN 6 | 221,222 | 68 | 1754.5 | 9608 | 2051 | |
HQ 7 | 11,643 | 72 | 1780.5 | 6442 | 2053 | |
LQ 8 | 14 | 321 | 1883.8 | 3922 | 1839 | |
NH 2 | Subreads | 15,425,110 | 50 | 1491.4 | 115,220 | 1656 |
CCS | 420,743 | 67 | 1755.3 | 11,556 | 1939 | |
FL | 345,977 | 102 | 1613.7 | 9605 | 1735 | |
FLCN | 308,364 | 51 | 1495.2 | 9573 | 1534 | |
HQ | 16,587 | 70 | 1630.5 | 6778 | 2012 | |
LQ | 12 | 452 | 857.1 | 1617 | 951 | |
DH 3 | Subreads | 15,459,279 | 50 | 1437.4 | 118,301 | 1590 |
CCS | 367,638 | 70 | 1782.2 | 14,497 | 1994 | |
FL | 253,545 | 104 | 1683.4 | 11,344 | 1926 | |
FLCN | 221,371 | 50 | 1568.1 | 9804 | 1769 | |
HQ | 10,336 | 69 | 1661.6 | 6526 | 2132 | |
LQ | 9 | 115 | 604.1 | 1880 | 654 |
Samples | Numbers of Transcript Isoforms after Collapsing Redundant Isoforms | Length of Collapsing Redundant Isoforms | N50 4 | |||||
---|---|---|---|---|---|---|---|---|
Reference Genome | Fake Genome | Unmap-Ped | Merge | Min | Max | Mean | ||
SPA 1 | 9427 | 466 | 2 | 9872 | 92 | 6442 | 1798.9 | 2079 |
NH 2 | 11,639 | 752 | 3 | 12,382 | 118 | 6778 | 1663.6 | 2041 |
DH 3 | 7858 | 661 | 3 | 8508 | 80 | 6526 | 1685.5 | 2161 |
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Ye, S.; Yu, X.; Chen, H.; Zhang, Y.; Wu, Q.; Tan, H.; Song, J.; Saqib, H.S.A.; Farhadi, A.; Ikhwanuddin, M.; et al. Full-Length Transcriptome Reconstruction Reveals the Genetic Mechanisms of Eyestalk Displacement and Its Potential Implications on the Interspecific Hybrid Crab (Scylla serrata ♀ × S. paramamosain ♂). Biology 2022, 11, 1026. https://doi.org/10.3390/biology11071026
Ye S, Yu X, Chen H, Zhang Y, Wu Q, Tan H, Song J, Saqib HSA, Farhadi A, Ikhwanuddin M, et al. Full-Length Transcriptome Reconstruction Reveals the Genetic Mechanisms of Eyestalk Displacement and Its Potential Implications on the Interspecific Hybrid Crab (Scylla serrata ♀ × S. paramamosain ♂). Biology. 2022; 11(7):1026. https://doi.org/10.3390/biology11071026
Chicago/Turabian StyleYe, Shaopan, Xiaoyan Yu, Huiying Chen, Yin Zhang, Qingyang Wu, Huaqiang Tan, Jun Song, Hafiz Sohaib Ahmed Saqib, Ardavan Farhadi, Mhd Ikhwanuddin, and et al. 2022. "Full-Length Transcriptome Reconstruction Reveals the Genetic Mechanisms of Eyestalk Displacement and Its Potential Implications on the Interspecific Hybrid Crab (Scylla serrata ♀ × S. paramamosain ♂)" Biology 11, no. 7: 1026. https://doi.org/10.3390/biology11071026
APA StyleYe, S., Yu, X., Chen, H., Zhang, Y., Wu, Q., Tan, H., Song, J., Saqib, H. S. A., Farhadi, A., Ikhwanuddin, M., & Ma, H. (2022). Full-Length Transcriptome Reconstruction Reveals the Genetic Mechanisms of Eyestalk Displacement and Its Potential Implications on the Interspecific Hybrid Crab (Scylla serrata ♀ × S. paramamosain ♂). Biology, 11(7), 1026. https://doi.org/10.3390/biology11071026