Transcriptome Profiling Provides Insight into the Genes in Carotenoid Biosynthesis during the Mesocarp and Seed Developmental Stages of Avocado (Persea americana)
Abstract
:1. Introduction
2. Results
2.1. Overview of the Morphology and NGST Profiling
2.2. Annotation and Identification of Unigenes
2.3. Screening of Differentially Expressed Genes during Avocado Mesocarp and Seed Development
2.4. Differentially Expressed Carotenoid Biosynthetic Genes between the Avocado Mesocarp and Seed
2.5. General Properties of Single-Molecule Long-Reads
2.6. Isoforms in Carotenoid Biosynthetic Pathway between the Avocado Mesocarp and Seed
2.7. Verification of Transcriptome Profiling in Carotenoid Biosynthetic Pathway between the Avocado Mesocarp and Seed by Metabolite Profiling via HPLC
3. Discussion
4. Materials and Methods
4.1. Plant Materials
4.2. NGST Sequencing
4.3. Transcriptome Assembly, Annotation, and Coding Sequence Prediction
4.4. Identification of Differentially Expressed Genes
4.5. Validation of Transcripts by Quantitative Real-Time PCR
4.6. SMRT Sequencing
4.7. Quality Filtering and Correction of PacBio Long-Reads
4.8. Analysis of Alpha- and Beta-Carotenes by HPLC
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Gene Name | Functional Protein Name | Enzyme Commission Number | Unigene ID |
---|---|---|---|
PaPSY | 15-cis-phytoene synthase | 2.5.1.32 | c103350.graph_c0, c113873.graph_c5 |
PaPDS | Phytoene desaturase | 1.3.5.5 | c103201.graph_c0, c104826.graph_c4 |
PaZ-ISO | 15-cis-ζ-carotene isomerase | 5.2.1.12 | c109620.graph_c1 |
PaZDS | ζ-carotene desaturase | 1.3.5.6 | c108741.graph_c1, c115069.graph_c3 |
PaCRTISO | Carotenoid isomerase | 5.2.1.13 | c108133.graph_c1 |
PaLCY-E | Lycopene ε-cyclase | 5.5.1.18 | c117627.graph_c3 |
PaLCY-B | Lycopene β-cyclase | 5.5.1.19 | c92930.graph_c0, c110018.graph_c0 |
PaCYP97A | P450 β-ring carotene hydroxylase | 1.14.13.129 | c106779.graph_c0 |
PaCYP97C | P450 ε-ring carotene hydroxylase | 1.14.99.45 | c110544.graph_c0 |
PaZEP | Zeaxanthin epoxidase | 1.14.15.21 | c109893.graph_c0, c116714.graph_c5 |
PaNSY | Neoxanthin synthase | 5.3.99.9 | c106233.graph_c1, c92501.graph_c0 |
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Ge, Y.; Cheng, Z.; Si, X.; Ma, W.; Tan, L.; Zang, X.; Wu, B.; Xu, Z.; Wang, N.; Zhou, Z.; et al. Transcriptome Profiling Provides Insight into the Genes in Carotenoid Biosynthesis during the Mesocarp and Seed Developmental Stages of Avocado (Persea americana). Int. J. Mol. Sci. 2019, 20, 4117. https://doi.org/10.3390/ijms20174117
Ge Y, Cheng Z, Si X, Ma W, Tan L, Zang X, Wu B, Xu Z, Wang N, Zhou Z, et al. Transcriptome Profiling Provides Insight into the Genes in Carotenoid Biosynthesis during the Mesocarp and Seed Developmental Stages of Avocado (Persea americana). International Journal of Molecular Sciences. 2019; 20(17):4117. https://doi.org/10.3390/ijms20174117
Chicago/Turabian StyleGe, Yu, Zhihao Cheng, Xiongyuan Si, Weihong Ma, Lin Tan, Xiaoping Zang, Bin Wu, Zining Xu, Nan Wang, Zhaoxi Zhou, and et al. 2019. "Transcriptome Profiling Provides Insight into the Genes in Carotenoid Biosynthesis during the Mesocarp and Seed Developmental Stages of Avocado (Persea americana)" International Journal of Molecular Sciences 20, no. 17: 4117. https://doi.org/10.3390/ijms20174117