Genome-Wide Analysis of the Trehalose-6-Phosphate Synthase Gene Family in Rose (Rosa chinensis) and Differential Expression under Heat Stress
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials and Heat Stress Experiment
2.2. Trehalose Content Detection in R. chinensis
2.3. Identification of Rose TPS Genes
2.4. Multiple Sequence Alignment and Phylogenetic Analysis
2.5. Selective Pressure Analysis
2.6. Protein Physicochemical Properties and Subcellular Localization Analysis
2.7. TPS Gene Structure and Cis-Acting Element Analyses
2.8. Protein Motif and Conserved Domain Analysis
2.9. Gene Chromosomal Location and Collinearity Analysis
2.10. Real-Time Quantitative PCR
3. Results
3.1. Dynamics of the Trehalose Levels in the Leaf, Stem, and Root Tissues of R. chinensis under Heat Stress
3.2. Identification and Analysis of the Characteristics of TPS Family Members in R. chinensis
3.3. Gene Structure and cis-Acting Element Analyses of RcTPS Genes
3.4. Protein Domain Analyses and Multiple Sequence Alignment of the TPS Family in R. chinensis
3.5. Evolution Analysis of RcTPS Genes
3.6. Expression Pattern Analysis of RcTPS Genes under Heat Stress
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Gene | Scaffold ID | Predicted Position | CDS (bp) | Deduced Polypeptide | Predicted Subcellular Localization | |||
---|---|---|---|---|---|---|---|---|
Length (aa) | MW (kDa) | pI | GRAVY | |||||
RcTPS1a | Scaffold_5 | 8460464–8470382 | 2934 | 977 | 109.54 | 6.03 | −0.290 | Nuclear |
RcTPS1b | Scaffold_5 | 23007334–23020393 | 2793 | 930 | 105.29 | 6.23 | −0.391 | Nuclear |
RcTPS5 | Scaffold_7 | 27956967–27962352 | 2586 | 861 | 97.30 | 5.71 | −0.164 | Cytoplasmic |
RcTPS6 | Scaffold_4 | 64110270–64114733 | 2565 | 854 | 96.75 | 5.84 | −0.184 | Nuclear |
RcTPS7a | Scaffold_2 | 47116733–47121620 | 2664 | 887 | 101.08 | 6.18 | −0.264 | Cytoplasmic |
RcTPS7b | Scaffold_5 | 7851849–7856449 | 2565 | 854 | 96.32 | 5.87 | −0.266 | Cytoplasmic |
RcTPS9 | Scaffold_7 | 12207610–12212604 | 2592 | 863 | 98.38 | 6.11 | −0.224 | Cytoplasmic |
RcTPS10 | Scaffold_4 | 64989897–64994372 | 2601 | 866 | 97.48 | 5.85 | −0.205 | Cytoplasmic |
RcTPS11 | Scaffold_4 | 24462064–24465676 | 2637 | 878 | 99.56 | 5.89 | −0.203 | Cytoplasmic |
Group | N a | dN/dS(ω) under M0 | 2Δ/M3 vs. M0 b | 2Δ/M8 vs. M7 | M8 Estimates | Selective Position |
---|---|---|---|---|---|---|
I | 17 | 0.09691 | 295.922 ** | 44.089 | p1 = 0.02814 ω = 2.49539 (p = 0.59741 q = 5.21453) | 137L, 255S, 388D, 401I, 435P, 503E, 562D *, 632N, 637S, 639Q, 679S |
II1 | 18 | 0.05352 | 475.124 ** | 17.556 | p1 = 0.01043 ω = 7.57672 (p = 0.26744 q = 3.43511) | 300K, 426A |
II2 | 16 | 0.08810 | 339.810 ** | 25.457 | p1 = 0.03229 ω = 3.83594 (p = 0.36190 q = 3.30447) | 3L, 54S, 166S, 228R, 409L, 476A, 482R, 506A, 552Q, 682L, 685I, 691S, 716N |
II3 | 19 | 0.11694 | 712.521 ** | 34.111 | p1 = 0.02958 ω = 9.36648 (p = 0.44335 q = 2.88651) | 25A, 44Y, 622T, 771I, 772M * |
II4 | 8 | 0.09783 | 318.212 ** | 28.595 | p1 = 0.05407 ω = 2.40780 (p = 0.44632 q = 4.10918) | 20N, 39V, 40P, 46S, 65A, 88K, 113S, 128M, 307E, 315Q, 458D, 459R, 504A, 542R, 630L, 656T, 752Q, 780S, 781S, 786V, 825S, 826T, 828P, 829K, 830L |
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Wei, X.-R.; Ling, W.; Ma, Y.-W.; Du, J.-L.; Cao, F.-X.; Chen, H.-X.; Chen, J.-R.; Li, Y.-F. Genome-Wide Analysis of the Trehalose-6-Phosphate Synthase Gene Family in Rose (Rosa chinensis) and Differential Expression under Heat Stress. Horticulturae 2022, 8, 429. https://doi.org/10.3390/horticulturae8050429
Wei X-R, Ling W, Ma Y-W, Du J-L, Cao F-X, Chen H-X, Chen J-R, Li Y-F. Genome-Wide Analysis of the Trehalose-6-Phosphate Synthase Gene Family in Rose (Rosa chinensis) and Differential Expression under Heat Stress. Horticulturae. 2022; 8(5):429. https://doi.org/10.3390/horticulturae8050429
Chicago/Turabian StyleWei, Xiao-Ru, Wu Ling, Yu-Wan Ma, Jiao-Lin Du, Fu-Xiang Cao, Hai-Xia Chen, Ji-Ren Chen, and Yu-Fan Li. 2022. "Genome-Wide Analysis of the Trehalose-6-Phosphate Synthase Gene Family in Rose (Rosa chinensis) and Differential Expression under Heat Stress" Horticulturae 8, no. 5: 429. https://doi.org/10.3390/horticulturae8050429
APA StyleWei, X. -R., Ling, W., Ma, Y. -W., Du, J. -L., Cao, F. -X., Chen, H. -X., Chen, J. -R., & Li, Y. -F. (2022). Genome-Wide Analysis of the Trehalose-6-Phosphate Synthase Gene Family in Rose (Rosa chinensis) and Differential Expression under Heat Stress. Horticulturae, 8(5), 429. https://doi.org/10.3390/horticulturae8050429