Genome-Wide Identification of the WUSCHEL-Related Homeobox (WOX) Gene Family in Three Cymbidium Species and Expression Patterns in C. goeringii
Abstract
:1. Introduction
2. Materials and Methods
2.1. Identification of the WOX Genes
2.2. Phylogenetic Analysis and Physicochemical Properties
2.3. Conserved Motif, Gene Structure Analysis, and Cis-Acting Element Prediction
2.4. Chromosome Location and Collinearity Analysis
2.5. RNA Extraction and RT-qPCR Analysis
3. Results
3.1. Phylogeny Analysis of the WOX Genes
3.2. Identification and Characterization of the WOX Genes in Three Cymbidium Species
3.3. Sequence Alignment, Gene Structure, and Conserved Motif Analysis of WOX Genes
3.4. Chromosomal Localization and Collinearity Analysis of WOX Genes
3.5. Cis-Acting Element Analysis of Three Cymbidium Species
3.6. Expression Patterns and qRT-PCR Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Gene Name | Gene ID | Number of Amino Acids (AA) | Theoretical PI | Molecular Weight (Mw) | Instability Index (II) | Aliphatic Index (AI) | Grand Average of Hydropathicity (GRAVY) | Clade | Subcellular Localization |
---|---|---|---|---|---|---|---|---|---|
CgWOX1 | GL10772 | 267 | 5.17 | 28,478.85 | 64.82 | 73.52 | −0.194 | Intermediate | Nucleus |
CgWOX2 | GL12480 | 246 | 6.46 | 28,129.68 | 66.80 | 65.45 | −0.725 | Ancient | Nucleus |
CgWOX3 | GL01022 | 185 | 8.5 | 21,245.19 | 56.37 | 64.81 | −0.685 | WUS | Nucleus |
CgWOX4 | GL17509 | 270 | 6.16 | 29,728.17 | 68.62 | 77.59 | −0.366 | Intermediate | Nucleus |
CgWOX5 | GL12104 | 265 | 5.69 | 30,696.42 | 72.51 | 59.66 | −0.908 | WUS | Nucleus |
CgWOX6 | GL17950 | 193 | 9.04 | 21,862.46 | 69.93 | 50.57 | −0.798 | WUS | Nucleus |
CgWOX7 | GL20683 | 334 | 7.76 | 36,147.56 | 52.44 | 78.02 | −0.295 | Intermediate | Nucleus |
CgWOX8 | GL21289 | 199 | 5.78 | 22,446.3 | 74.02 | 69.20 | −0.716 | Ancient | Nucleus |
CeWOX1 | JL010469 | 259 | 5.13 | 27,488.5 | 66.44 | 70.15 | −0.283 | Intermediate | Nucleus |
CeWOX2 | JL008369 | 164 | 9.73 | 19,245.09 | 48.15 | 86.89 | −0.416 | WUS | Nucleus |
CeWOX3 | JL002473 | 246 | 6.26 | 28,201.74 | 67.93 | 65.45 | −0.737 | Ancient | Nucleus |
CeWOX4 | JL000437 | 249 | 8.29 | 28,049.87 | 71.75 | 70.88 | −0.576 | WUS | Nucleus |
CeWOX5 | JL017101 | 249 | 5.95 | 27,247.28 | 68.05 | 70.84 | −0.418 | Intermediate | Nucleus |
CeWOX6 | JL014141 | 212 | 6.05 | 24,084.04 | 79.61 | 57.08 | −0.753 | WUS | Nucleus |
CeWOX7 | JL011816 | 143 | 10.13 | 16,583.28 | 60.02 | 72.94 | −0.691 | WUS | Nucleus |
CeWOX8 | JL011815 | 149 | 7.06 | 17,178.42 | 45.65 | 62.15 | −0.692 | WUS | Nucleus |
CeWOX9 | JL017647 | 108 | 10.28 | 12,931.8 | 75.10 | 56.85 | −0.780 | WUS | Nucleus |
CeWOX10 | JL000993 | 198 | 4.89 | 22,612.75 | 68.78 | 54.80 | −0.956 | WUS | Nucleus |
CeWOX11 | JL000483 | 255 | 5.26 | 28,775.24 | 69.52 | 65.45 | −0.709 | Ancient | Nucleus |
CeWOX12 | JL015470 | 335 | 7.76 | 36,218.63 | 52.31 | 78.09 | −0.289 | Intermediate | Nucleus |
CsWOX1 | cymsin_Mol009245 | 102 | 9.88 | 12,008.36 | 62.39 | 60.29 | −1.154 | WUS | Nucleus |
CsWOX2 | cymsin_Mol021168 | 177 | 9.14 | 20,024.33 | 60.67 | 51.30 | −0.801 | WUS | Nucleus |
CsWOX3 | cymsin_Mol007512 | 249 | 8.76 | 27,992.9 | 70.28 | 69.32 | −0.573 | WUS | Nucleus |
CsWOX4 | cymsin_Mol017948 | 246 | 6.09 | 28,160.71 | 68.71 | 64.27 | −0.735 | Ancient | Nucleus |
CsWOX5 | cymsin_Mol019643 | 212 | 6.23 | 24,098.11 | 79.39 | 57.08 | −0.767 | WUS | Nucleus |
CsWOX6 | cymsin_Mol006735 | 128 | 11.63 | 14,521.36 | 77.48 | 72.42 | −0.766 | Intermediate | Nucleus |
CsWOX7 | cymsin_Mol012795 | 194 | 9.6 | 21,959.27 | 40.74 | 76.86 | −0.375 | WUS | Nucleus |
CsWOX8 | cymsin_Mol012174 | 228 | 5.9 | 25,686.97 | 66.95 | 68.46 | −0.606 | Ancient | Nucleus |
CsWOX9 | cymsin_Mol005406 | 334 | 7.77 | 36,197.62 | 51.70 | 78.02 | −0.302 | Intermediate | Nucleus |
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Wang, F.; Chen, X.; Cheng, M.; Zhou, C.; Zheng, R.; Wu, X.; Duan, Y.; Ahmad, S.; Liu, Z.; Chen, J.; et al. Genome-Wide Identification of the WUSCHEL-Related Homeobox (WOX) Gene Family in Three Cymbidium Species and Expression Patterns in C. goeringii. Horticulturae 2024, 10, 645. https://doi.org/10.3390/horticulturae10060645
Wang F, Chen X, Cheng M, Zhou C, Zheng R, Wu X, Duan Y, Ahmad S, Liu Z, Chen J, et al. Genome-Wide Identification of the WUSCHEL-Related Homeobox (WOX) Gene Family in Three Cymbidium Species and Expression Patterns in C. goeringii. Horticulturae. 2024; 10(6):645. https://doi.org/10.3390/horticulturae10060645
Chicago/Turabian StyleWang, Fei, Xiuming Chen, Mengya Cheng, Chengcheng Zhou, Ruiyue Zheng, Xiaopei Wu, Yanru Duan, Sagheer Ahmad, Zhongjian Liu, Jinliao Chen, and et al. 2024. "Genome-Wide Identification of the WUSCHEL-Related Homeobox (WOX) Gene Family in Three Cymbidium Species and Expression Patterns in C. goeringii" Horticulturae 10, no. 6: 645. https://doi.org/10.3390/horticulturae10060645
APA StyleWang, F., Chen, X., Cheng, M., Zhou, C., Zheng, R., Wu, X., Duan, Y., Ahmad, S., Liu, Z., Chen, J., & Peng, D. (2024). Genome-Wide Identification of the WUSCHEL-Related Homeobox (WOX) Gene Family in Three Cymbidium Species and Expression Patterns in C. goeringii. Horticulturae, 10(6), 645. https://doi.org/10.3390/horticulturae10060645