Genome-Wide Analysis of the Sucrose Synthase Gene Family in Grape (Vitis vinifera): Structure, Evolution, and Expression Profiles
Abstract
:1. Introduction
2. Methods
2.1. Mining of Grape Sucrose Synthase Genes
2.2. Chromosomal Localization and Syntenic Analysis
2.3. Gene Structure and Phylogenetic Analysis
2.4. Ratio of Nonsynonymous to Synonymous Substitutions (dN/dS) and Relative Evolutionary Rate Test
2.5. Microarray Data Analysis
2.6. Plant Material and Treatments
2.7. RNA Extraction, cDNA Synthesis and Quantitative Real-Time PCR (qRT-PCR)
3. Results
3.1. Characteristics of the Grapevine Sucrose Synthase Gene Family
3.2. Exon/intron Organization of the Grapevine Sucrose Synthase Gene Family
3.3. Gene Duplication and Syntenic Analysis of the Grapevine Sucrose Synthase Genes
3.4. Phylogenetic Analysis of the Grapevine Sucrose Synthase Genes
3.5. Evolution of the Coding Sequences of the Grape SS Gene Pairs
3.6. Expression Analysis of VvSS Genes in Different Organs, Tissues and Developmental Stages
3.7. Expression Patterns of VvSS Genes in Response to Biotic and Abiotic Stresses
4. Discussion
4.1. Evolutionary Conservation and Divergence Among Grape SS Genes
4.2. VvSS Genes Involved in Grapevine Growth and Development
4.3. Stress Induced VvSS Expression in Grapevine
5. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Name | Locus Id a | Genomic DNA Size (bp) | CDS Size (bp) | Number of Amino Acids | Predicted Mw (kDa) | Theoretical pI | Ai | GRAVY | Chromosome Location | Group | Functional Domains (Start–End, bp) | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
Sucrose Synthase | Glycosyl Transferase | |||||||||||
VvSS1 | VIT_204s0079g00230 | 4513 | 2457 | 840 | 95.4 | 8.28 | 83.49 | −0.339 | chr4:10519070-10523582 | II | 9-557 | 569-745 |
VvSS2 | VIT_205s0077g01930 | 7914 | 2508 | 835 | 95.6 | 5.85 | 91.99 | −0.244 | chr5:1507610-1515524 | I | 8-553 | 566-765 |
VvSS3 | VIT_207s0005g00750 | 9214 | 2436 | 811 | 92.4 | 5.73 | 90.49 | −0.254 | chr7:3380739-3389952 | I | 8-555 | 568-741 |
VvSS4 | VIT_211s0016g00470 | 4229 | 2448 | 815 | 93.6 | 6.13 | 92.20 | −0.247 | chr11:489955-494383 | I | 9-553 | 565--740 |
VvSS5 | VIT_217s0053g00700 | 4820 | 2610 | 906 | 102.7 | 7.55 | 81.19 | −0.359 | chr17:15994677-15999496 | II | 12-558 | 568-736 |
VvSS1 | VvSS2 | VvSS3 | VvSS4 | VvSS5 | |
---|---|---|---|---|---|
VvSS1 | - | 51.79 | 53.81 | 53.45 | 70.56 |
VvSS2 | 59.18 | - | 79.12 | 66.86 | 47.70 |
VvSS3 | 59.93 | 77.55 | - | 71.15 | 50.00 |
VvSS4 | 59.60 | 66.36 | 69.47 | - | 59.57 |
VvSS5 | 70.50 | 54.85 | 56.60 | 56.85 | - |
Gene 1 | Gene 2 | dN | dS | dN/dS |
---|---|---|---|---|
VvSS2 | VvSS3 | 0.3012 | 0.0957 | 3.1473 |
VvSS1 | VvSS5 | 0.2759 | 0.1246 | 2.2143 |
Testing Group | Mt b | M1 c | M2 d | X2 | P e |
---|---|---|---|---|---|
VvSS2/VvSS3 with GmSS2 | 586 | 11 | 30 | 8.91 | 0.00450 |
VvSS1/VvSS5 with GmSS4 | 472 | 9 | 4 | 1.92 | 0.21690 |
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Zhu, X.; Wang, M.; Li, X.; Jiu, S.; Wang, C.; Fang, J. Genome-Wide Analysis of the Sucrose Synthase Gene Family in Grape (Vitis vinifera): Structure, Evolution, and Expression Profiles. Genes 2017, 8, 111. https://doi.org/10.3390/genes8040111
Zhu X, Wang M, Li X, Jiu S, Wang C, Fang J. Genome-Wide Analysis of the Sucrose Synthase Gene Family in Grape (Vitis vinifera): Structure, Evolution, and Expression Profiles. Genes. 2017; 8(4):111. https://doi.org/10.3390/genes8040111
Chicago/Turabian StyleZhu, Xudong, Mengqi Wang, Xiaopeng Li, Songtao Jiu, Chen Wang, and Jinggui Fang. 2017. "Genome-Wide Analysis of the Sucrose Synthase Gene Family in Grape (Vitis vinifera): Structure, Evolution, and Expression Profiles" Genes 8, no. 4: 111. https://doi.org/10.3390/genes8040111
APA StyleZhu, X., Wang, M., Li, X., Jiu, S., Wang, C., & Fang, J. (2017). Genome-Wide Analysis of the Sucrose Synthase Gene Family in Grape (Vitis vinifera): Structure, Evolution, and Expression Profiles. Genes, 8(4), 111. https://doi.org/10.3390/genes8040111