Transcriptome Sequencing and De Novo Assembly of Golden Cuttlefish Sepia esculenta Hoyle
Abstract
:1. Introduction
2. Results
2.1. Illumina Sequencing and Assembly
2.2. Functional Categorization
2.3. Differentially Transcribed Genes among Cleavage Stage Embryos and Healthy Larvae
2.4. Signaling Pathways Related to Embryo Development
3. Discussion
4. Experimental Section
4.1. Sample Collection
4.2. RNA Isolation and Illumina Sequencing
4.3. Transcriptome Assembly
4.4. Gene Annotation
4.5. Differential Gene Expression Analysis
4.6. Quantitative Real Time PCR
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Statistics of Sequencing Data | Numbers |
---|---|
Raw reads of mRNA-Seq | 32,597,241 |
Clean reads of mRNA-Seq | 31,840,631 (97.7%) |
Unigenes assembled | 98,615 |
Total length of unigenes (bp) | 61,246,386 |
Ave. length of unigenes (bp) | 621 |
N50 length of unigenes (bp) | 911 |
Max. length of unigenes (bp) | 19,292 |
Min. length of unigenes (bp) | 201 |
Raw reads of the three DGE samples | 7,671,799 a/9,439,043 b/8,512,259 c |
Clean reads of the three DGE samples | 7,562,335 a/9,305,149 b/8,376,805 c |
Databases | Number of Unigenes | Percentage (%) |
---|---|---|
Annotated in NR 1 | 18,921 | 19.2 |
Annotated in NT 2 | 2720 | 2.8 |
Annotated in KEGG 3 | 7761 | 7.9 |
Annotated in SwissProt | 15,078 | 15.3 |
Annotated in PFAM 4 | 19,150 | 19.4 |
Annotated in GO | 19,643 | 19.9 |
Annotated in KOG 5 | 10,547 | 10.7 |
Annotated in all databases | 1516 | 1.5 |
Annotated in least one database | 25,462 | 25.8 |
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Liu, C.; Zhao, F.; Yan, J.; Liu, C.; Liu, S.; Chen, S. Transcriptome Sequencing and De Novo Assembly of Golden Cuttlefish Sepia esculenta Hoyle. Int. J. Mol. Sci. 2016, 17, 1749. https://doi.org/10.3390/ijms17101749
Liu C, Zhao F, Yan J, Liu C, Liu S, Chen S. Transcriptome Sequencing and De Novo Assembly of Golden Cuttlefish Sepia esculenta Hoyle. International Journal of Molecular Sciences. 2016; 17(10):1749. https://doi.org/10.3390/ijms17101749
Chicago/Turabian StyleLiu, Changlin, Fazhen Zhao, Jingping Yan, Chunsheng Liu, Siwei Liu, and Siqing Chen. 2016. "Transcriptome Sequencing and De Novo Assembly of Golden Cuttlefish Sepia esculenta Hoyle" International Journal of Molecular Sciences 17, no. 10: 1749. https://doi.org/10.3390/ijms17101749