De Novo Characterization of Flower Bud Transcriptomes and the Development of EST-SSR Markers for the Endangered Tree Tapiscia sinensis
Abstract
:1. Introduction
2. Results and Discussion
2.1. Sequencing and de novo Assembly
2.2. Sequence Annotation and Classification
2.3. Genes Putatively Related to Flower Development
2.4. SSR Mining from the T. sinensis Transcriptome
Item | Number |
---|---|
Total number of sequences examined | 52,169 |
Total size of examined sequences (bp) | 58,253,075 |
Total number of identified SSRs | 10,371 |
Number of SSR containing sequences | 8608 |
Number of sequences containing more than 1 SSR | 1436 |
Number of SSRs present in compound formation | 733 |
Repeat Numbers | Motif | Total | Repeat Number (%) | ||||
---|---|---|---|---|---|---|---|
Di- | Tri- | Tetra- | Penta- | Hexa | |||
4 | 0 | 0 | 368 | 158 | 266 | 792 | 7.64 |
5 | 0 | 1319 | 101 | 15 | 12 | 1447 | 13.95 |
6 | 2026 | 703 | 52 | 5 | 11 | 2797 | 26.97 |
7 | 1416 | 411 | 0 | 0 | 4 | 1831 | 17.66 |
8 | 1164 | 49 | 1 | 1 | 2 | 1217 | 11.73 |
9 | 1256 | 0 | 0 | 0 | 0 | 1256 | 12.11 |
10 | 823 | 1 | 0 | 0 | 0 | 824 | 7.95 |
11 | 195 | 1 | 0 | 0 | 0 | 196 | 1.89 |
˃11 | 8 | 2 | 0 | 0 | 1 | 11 | 0.11 |
Total | 6888 | 2486 | 522 | 179 | 296 | 10,371 | 100 |
Motif (%) | 66.42 | 23.97 | 5.03 | 1.73 | 2.85 |
2.5. SSR Marker Assessment and Application
Primer | Motif | K | HO | HE | PIC | HW |
---|---|---|---|---|---|---|
TS053 | (TCA)6 | 9 | 0.706 | 0.835 | 0.804 | ND |
TS126 | (TAC)7 | 6 | 0.706 | 0.768 | 0.723 | NS |
TS103 | (AAGA)5 | 5 | 0.549 | 0.631 | 0.573 | NS |
TS149 | (TTG)11 | 6 | 0.608 | 0.769 | 0.725 | NS |
TS060 | (TGT)6 | 6 | 0.529 | 0.501 | 0.464 | NS |
TS013 | (AGA)8 | 5 | 0.51 | 0.653 | 0.592 | NS |
3. Materials and Methods
3.1. Plant Material and RNA Extraction
3.2. cDNA Library Construction and Illumina Sequencing
3.3. De Novo Assembly and Annotation
3.4. SSR Detection and Primer Design
3.5. SSR Validation and Assessment
4. Conclusions
Supplementary Files
Supplementary File 1Acknowledgments
Author Contributions
Conflicts of Interest
References
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Zhou, X.-J.; Wang, Y.-Y.; Xu, Y.-N.; Yan, R.-S.; Zhao, P.; Liu, W.-Z. De Novo Characterization of Flower Bud Transcriptomes and the Development of EST-SSR Markers for the Endangered Tree Tapiscia sinensis. Int. J. Mol. Sci. 2015, 16, 12855-12870. https://doi.org/10.3390/ijms160612855
Zhou X-J, Wang Y-Y, Xu Y-N, Yan R-S, Zhao P, Liu W-Z. De Novo Characterization of Flower Bud Transcriptomes and the Development of EST-SSR Markers for the Endangered Tree Tapiscia sinensis. International Journal of Molecular Sciences. 2015; 16(6):12855-12870. https://doi.org/10.3390/ijms160612855
Chicago/Turabian StyleZhou, Xiao-Jun, Yue-Yue Wang, Ya-Nan Xu, Rong-Shan Yan, Peng Zhao, and Wen-Zhe Liu. 2015. "De Novo Characterization of Flower Bud Transcriptomes and the Development of EST-SSR Markers for the Endangered Tree Tapiscia sinensis" International Journal of Molecular Sciences 16, no. 6: 12855-12870. https://doi.org/10.3390/ijms160612855
APA StyleZhou, X. -J., Wang, Y. -Y., Xu, Y. -N., Yan, R. -S., Zhao, P., & Liu, W. -Z. (2015). De Novo Characterization of Flower Bud Transcriptomes and the Development of EST-SSR Markers for the Endangered Tree Tapiscia sinensis. International Journal of Molecular Sciences, 16(6), 12855-12870. https://doi.org/10.3390/ijms160612855