Transcriptome Analysis of Carbohydrate Metabolism Genes and Molecular Regulation of Sucrose Transport Gene LoSUT on the Flowering Process of Developing Oriental Hybrid Lily ‘Sorbonne’ Bulb
Abstract
:1. Introduction
2. Results
2.1. Analysis of Carbohydrate Metabolism Gene Annotation
2.2. Analysis of Gene Expression Patterns of Carbohydrate Metabolism
2.3. Analysis of Co-Expression Patterns of Genes
2.4. Changes in Carbohydrate and Hormone Content
2.5. Analysis of SUT Gene and Carbohydrate Metabolism Genes, Flower Differentiation Genes and Hormone Genes Expression
2.6. Full Length Cloning of Genes
2.7. Evolutionary Tree
2.8. 3D Structural Models of Protein LoSUT2 and LoSUT4 and its Subcellular Localization in Onion Epidermis
2.9. Phenotypic Changes and Fluorescence Quantitative Analysis of Transgenic Arabidopsis thaliana
3. Discussion
3.1. Effects of SUT Genes on Bulb Development of Lily Together with Carbohydrate Metabolism Genes, Flower Genes and Hormone Genes
3.2. The SUT Full Length Sequences and its Genes Function in Oriental Lily
4. Materials and Methods
4.1. Plant Material
4.2. Analysis of Carbohydrate Metabolism Genes and Construction of Gene Co-Expression Network
4.3. Total RNA Isolation
4.4. Isolation of LoSUT2 Full-Length cDNA
4.5. Real-Time Quantitative PCR Verification
4.6. Protein Physical and Chemical Properties
4.7. Prediction of Protein Secondary Structure and Post-Translational Modification
4.8. Multiple Sequence Alignment and Construction of Phylogenetic Tree
4.9. Analysis of Soluble Sugars, Reducing Sugar and Sucrose
4.10. Analysis of Endogenous Hormones
4.11. Arabidopsis Transformation
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
Abbreviations
BLAST | Basic local alignment search tool; |
COG | Clusters of orthologous groups; |
DGE | Digital gene expression; |
EST | Expressed sequence tag; |
FDR | False discovery rate; |
GO | Gene ontology; |
KEGG | Kyoto Encyclopedia of Genes and Genomes Pathway; |
NCBI | National Center for Biotechnology Information; |
qRT-PCR | Real-time quantitative reverse transcription polymerase chain reaction; |
RACE | Rapid amplification of cDNA ends; |
RPKM | Number of reads per kilobase per million clean reads; |
SAM | Shoot apical meristem |
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Contig | All | All | Cell Wall | Acid | Vacuolar | Cytosolic | Neutral Alkaline | Neutral | |
---|---|---|---|---|---|---|---|---|---|
Contig88348 | 198|334 | 386 | Yes | Yes | Yes | Yes | CW, acid, Missing the front fragment | ||
Contig28073 | 197|334 | 237 | Yes | Yes | Yes | Yes | CWINV, Missing the back fragment | ||
Contig87326 | 186|334 | 140 | Yes | Yes | Yes | Yes | Not Suitable ORF | ||
Contig31833 | 156|334 | 100 | Yes | Yes | Yes | Yes | short fragment | ||
Contig1581 | 135|334 | 538 | Yes | Yes | Yes | NAINV, full length | |||
Contig8633 | 134|334 | 554 | Yes | Yes | Yes | Missing the front fragment, NAINV | |||
Contig11809 | 134|334 | 543 | Yes | Yes | Yes | NAINV, full length | |||
Contig6425 | 134|334 | 542 | Yes | Yes | Yes | NAINV, full length | |||
Contig17492 | 134|334 | 546 | Yes | Yes | Yes | NINV, full length | |||
Contig16491 | 134|334 | 498 | Yes | Yes | Yes | NINV, full length | |||
Contig28979 | 129|334 | 106 | Yes | Yes | Yes | NAINV, Only one small fragment later | |||
Contig84458 | 121|334 | 75 | Yes | Yes | Yes | Not Suitable ORF | |||
Contig43251 | 107|334 | 58 | Yes | Yes | Yes | Not Suitable ORF |
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Gu, J.; Zeng, Z.; Wang, Y.; Lyu, Y. Transcriptome Analysis of Carbohydrate Metabolism Genes and Molecular Regulation of Sucrose Transport Gene LoSUT on the Flowering Process of Developing Oriental Hybrid Lily ‘Sorbonne’ Bulb. Int. J. Mol. Sci. 2020, 21, 3092. https://doi.org/10.3390/ijms21093092
Gu J, Zeng Z, Wang Y, Lyu Y. Transcriptome Analysis of Carbohydrate Metabolism Genes and Molecular Regulation of Sucrose Transport Gene LoSUT on the Flowering Process of Developing Oriental Hybrid Lily ‘Sorbonne’ Bulb. International Journal of Molecular Sciences. 2020; 21(9):3092. https://doi.org/10.3390/ijms21093092
Chicago/Turabian StyleGu, Jiahui, Zhen Zeng, Yiru Wang, and Yingmin Lyu. 2020. "Transcriptome Analysis of Carbohydrate Metabolism Genes and Molecular Regulation of Sucrose Transport Gene LoSUT on the Flowering Process of Developing Oriental Hybrid Lily ‘Sorbonne’ Bulb" International Journal of Molecular Sciences 21, no. 9: 3092. https://doi.org/10.3390/ijms21093092