Comparative Transcriptome Analysis Combining SMRT- and Illumina-Based RNA-Seq Identifies Potential Candidate Genes Involved in Betalain Biosynthesis in Pitaya Fruit
Abstract
:1. Introduction
2. Result
2.1. The Variation of Pulp Color Parameters and Betalain Content
2.2. Transcriptome Analysis Using PacBio Sequel
2.3. Comparison of SMRT Sequencing and Next-Generation Sequencing
2.4. Clustering Analysis
2.5. Function Annotation
2.6. SSR and lncRNA Prediction
2.7. Genes Involved in Betalain Biosynthesis
3. Discussion
4. Material and Methods
4.1. Plant Materials
4.2. Measurements of Color and Betalain
4.3. RNA Sample Preparation
4.4. Library Preparation and SMRT Sequencing
4.5. Preprocessing of SMRT Reads
4.6. Functional Annotation of Genes
4.7. SSR Detection
4.8. lncRNAs Prediction
4.9. Next Generation Sequencing
4.10. Identification of DEGs Involved in Betalain Biosysthensis
4.11. Data Processing and Analysis
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Annotated-Database | Annotated-Number | Percentage (%) |
---|---|---|
COG-Annotation | 34,601 | 28.69 |
GO-Annotation | 54,706 | 45.36 |
KEGG-Annotation | 28,796 | 23.88 |
KOG-Annotation | 56,010 | 46.44 |
Pfam-Annotation | 88,549 | 73.42 |
Swissprot-Annotation | 72,130 | 59.81 |
TrEMBL-Annotation | 95,458 | 79.15 |
nr-Annotation | 105,413 | 87.40 |
nt-Annotation | 63,052 | 52.28 |
All-Annotation | 120,604 | 100.00 |
Gene | Gene ID | Gene | Gene ID |
---|---|---|---|
HpDODA1 | i1_LQ_R_c96099/f1p0/1004 | HpNAC | i1_HQ_R_c77544/f11p0/1295 |
HpDODA2 | i1_HQ_R_c9184/f4p0/1375 | HpCYP704C1 | i1_LQ_R_c24611/f1p0/1636 |
HpCYP76AD4 | i1_HQ_R_c13003/f5p0/1979 | HpFAR | i1_HQ_R_c76874/f3p0/1664 |
HpGSTs | i1_LQ_R_c13451/f1p0/1160 | HpSTK | i2_HQ_R_c697/f6p0/2233 |
HpBPE | i1_LQ_R_c9617/f1p0/1492 | HpVPP1 | i2_HQ_R_c679/f4p0/2556 |
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Wu, Y.; Xu, J.; Han, X.; Qiao, G.; Yang, K.; Wen, Z.; Wen, X. Comparative Transcriptome Analysis Combining SMRT- and Illumina-Based RNA-Seq Identifies Potential Candidate Genes Involved in Betalain Biosynthesis in Pitaya Fruit. Int. J. Mol. Sci. 2020, 21, 3288. https://doi.org/10.3390/ijms21093288
Wu Y, Xu J, Han X, Qiao G, Yang K, Wen Z, Wen X. Comparative Transcriptome Analysis Combining SMRT- and Illumina-Based RNA-Seq Identifies Potential Candidate Genes Involved in Betalain Biosynthesis in Pitaya Fruit. International Journal of Molecular Sciences. 2020; 21(9):3288. https://doi.org/10.3390/ijms21093288
Chicago/Turabian StyleWu, Yawei, Juan Xu, Xiumei Han, Guang Qiao, Kun Yang, Zhuang Wen, and Xiaopeng Wen. 2020. "Comparative Transcriptome Analysis Combining SMRT- and Illumina-Based RNA-Seq Identifies Potential Candidate Genes Involved in Betalain Biosynthesis in Pitaya Fruit" International Journal of Molecular Sciences 21, no. 9: 3288. https://doi.org/10.3390/ijms21093288
APA StyleWu, Y., Xu, J., Han, X., Qiao, G., Yang, K., Wen, Z., & Wen, X. (2020). Comparative Transcriptome Analysis Combining SMRT- and Illumina-Based RNA-Seq Identifies Potential Candidate Genes Involved in Betalain Biosynthesis in Pitaya Fruit. International Journal of Molecular Sciences, 21(9), 3288. https://doi.org/10.3390/ijms21093288