The Transcriptomes of the Crucian Carp Complex (Carassius auratus) Provide Insights into the Distinction between Unisexual Triploids and Sexual Diploids
Abstract
:1. Introduction
2. Results and Discussion
2.1. Transcriptome Sequencing and Assembly
2.2. Sequence Annotation and Validation
Database | Gibel Carp | Diploid Crucian Carp | |
---|---|---|---|
Homolog search | Fish Ensembl proteins | 32,030 | 31,620 |
Fish Ensembl transcripts | 13,513 | 10,956 | |
NCBI “nr” protein database | 235 | 56 | |
UTRdb | 852 | 1770 | |
NONCODE database | 336 | 491 | |
NCBI “nt” transcript database | 4004 | 1386 | |
ab initio prediction | BESTORF | 433 | 1260 |
Unknown | 3056 | 6300 | |
Total | 54,459 | 53,839 |
2.3. Genome Speciation Event Deduced from Orthologous Pairs
2.4. Low Tri-Allelic Polymorphism and Heterozygosity in Gibel Carp
2.5. Few Gene Expansions in Gibel Carp
Species | GO Term | GO ID | Percentage of Transcripts (%) * | p Value |
---|---|---|---|---|
Gibel carp | nucleic acid binding | GO:0003676 | 13.9:13.2 | 0.009 |
transferase activity | GO:0016740 | 10.4:9.8 | 0.012 | |
transferase activity, transferring phosphorus-containing groups | GO:0016772 | 6.6:6.2 | 0.028 | |
DNA binding | GO:0003677 | 7.6:7.1 | 0.033 | |
Diploid crucian carp | transporter activity | GO:0005215 | 4.1:4.7 | 0.000 |
transmembrane transporter activity | GO:0022857 | 3.2:3.9 | 0.000 | |
passive transmembrane transporter activity | GO:0022803 | 1.0:1.4 | 0.000 | |
substrate-specific transmembrane transporter activity | GO:0022891 | 2.7:3.3 | 0.000 | |
substrate-specific transporter activity | GO:0022892 | 4.1:4.7 | 0.001 |
Species | KEGG Pathway | Percentage of Gibel Carp Transcripts (%) | Percentage of Diploid Crucian Carp Transcripts (%) | p Value |
---|---|---|---|---|
Gibel carp | Ubiquitin mediated proteolysis | 1.70 | 1.38 | 0.013 |
Progesterone-mediated oocyte maturation | 1.13 | 0.89 | 0.018 | |
Fanconi anemia pathway | 0.61 | 0.46 | 0.038 | |
Diploid crucian carp | Neuroactive ligand-receptor interaction | 1.07 | 1.53 | 0.000 |
Cell adhesion molecules | 0.91 | 1.18 | 0.010 | |
Ribosome | 0.55 | 0.74 | 0.024 | |
Tight junction | 1.51 | 1.76 | 0.045 |
2.6. Differentially Expressed Orthologous Genes in Pooled Tissues and Gonads
3. Experimental Section
3.1. Sample Collection and Transcriptome Sequencing
3.2. Transcriptome Assembly, Annotation, and Validation
3.3. Genome Speciation Event Deduced from the Ks Distribution of Orthologous Pairs
3.4. The Analysis of Tri-Allelic Polymorphism and Heterozygosity in Gibel Carp
3.5. Gene Expansions in Special Molecular Functions and Pathways
3.6. Analysis and Validation of Differentially Expressed Orthologous Genes
4. Conclusions
Supplementary Files
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Li, C.-Y.; Li, J.-T.; Kuang, Y.-Y.; Xu, R.; Zhao, Z.-X.; Hou, G.-Y.; Liang, H.-W.; Sun, X.-W. The Transcriptomes of the Crucian Carp Complex (Carassius auratus) Provide Insights into the Distinction between Unisexual Triploids and Sexual Diploids. Int. J. Mol. Sci. 2014, 15, 9386-9406. https://doi.org/10.3390/ijms15069386
Li C-Y, Li J-T, Kuang Y-Y, Xu R, Zhao Z-X, Hou G-Y, Liang H-W, Sun X-W. The Transcriptomes of the Crucian Carp Complex (Carassius auratus) Provide Insights into the Distinction between Unisexual Triploids and Sexual Diploids. International Journal of Molecular Sciences. 2014; 15(6):9386-9406. https://doi.org/10.3390/ijms15069386
Chicago/Turabian StyleLi, Chun-Yan, Jiong-Tang Li, You-Yi Kuang, Ru Xu, Zi-Xia Zhao, Guang-Yuan Hou, Hong-Wei Liang, and Xiao-Wen Sun. 2014. "The Transcriptomes of the Crucian Carp Complex (Carassius auratus) Provide Insights into the Distinction between Unisexual Triploids and Sexual Diploids" International Journal of Molecular Sciences 15, no. 6: 9386-9406. https://doi.org/10.3390/ijms15069386