Genome-Wide Identification and Analysis of the MADS-Box Gene Family in Theobroma cacao
Abstract
:1. Introduction
2. Materials and Methods
2.1. Identification of MADS-Box Genes in Theobroma cacao
2.2. Phylogenetic Analysis and Classification of MADS-Box Genes
2.3. Conserved Motif and Gene Structure Analysis
2.4. Chromosomal Localization and Gene Duplication
2.5. Analysis of Cis-Acting Element in MADS-Box Genes’ Promoters
3. Results
3.1. Identification of MADS-Box Genes in Theobroma cacao
3.2. Phylogenetic Analysis and Classification of the MADS-Box Gene
3.3. Conserved Motif and Structure Analysis
3.4. Genome Distribution and Gene Evolution Analysis of TcMADS Genes
3.5. Analysis of Putative Promoter Regions in TcMADS Genes
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene Name | Gene ID | Physicochemical Characteristics | SL | ORF | ||||
---|---|---|---|---|---|---|---|---|
PI | MW (Da) | Length (aa) | Instability Index | Aliphatic Index | ||||
TcMADS1 | TCM_000239 | 9.48 | 46,436.9 | 406 | 39.09 | 77.32 | nucleus | 1221 |
TcMADS2 | TCM_000266 | 9.59 | 26,095.8 | 224 | 46.52 | 87.1 | chloroplast | 675 |
TcMADS3 | TCM_000725 | 9.91 | 36,097.68 | 315 | 58.23 | 83.87 | nucleus | 948 |
TcMADS4 | TCM_000878 | 6.85 | 26,140.89 | 237 | 41.11 | 78.23 | chloroplast | 714 |
TcMADS5 | TCM_000931 | 9.12 | 29,034.14 | 250 | 45.33 | 84.56 | chloroplast | 753 |
TcMADS6 | TCM_000992 | 6.55 | 25,353.79 | 224 | 53.32 | 85.76 | nucleus | 675 |
TcMADS7 | TCM_001181 | 5.86 | 66,752.75 | 600 | 48.76 | 77.52 | nucleus | 1803 |
TcMADS8 | TCM_001182 | 5.43 | 37,831.38 | 337 | 62.2 | 73.77 | nucleus | 1014 |
TcMADS9 | TCM_001335 | 9.19 | 38,279.15 | 338 | 38.49 | 68.11 | nucleus | 1017 |
TcMADS10 | TCM_001841 | 9.85 | 31,109.18 | 269 | 62.98 | 6.17 | chloroplast | 810 |
TcMADS11 | TCM_005456 | 8.91 | 30,163.08 | 262 | 53.63 | 84.89 | endomembrane system | 789 |
TcMADS12 | TCM_005458 | 9.08 | 27,810.84 | 243 | 38.49 | 82.3 | nucleus | 732 |
TcMADS13 | TCM_005818 | 8.51 | 42,280.27 | 375 | 42.75 | 101.09 | nucleus | 1128 |
TcMADS14 | TCM_006323 | 9.42 | 28,732.02 | 254 | 52.22 | 62.24 | nucleus | 765 |
TcMADS15 | TCM_006324 | 9.15 | 27,699.77 | 243 | 43.97 | 85.56 | nucleus | 732 |
TcMADS16 | TCM_006325 | 5.42 | 24,228.12 | 218 | 45.89 | 55.96 | nucleus | 657 |
TcMADS17 | TCM_007324 | 9.52 | 20,330.45 | 174 | 48.32 | 100.29 | chloroplast | 525 |
TcMADS18 | TCM_007378 | 8.96 | 24,754.12 | 219 | 51.13 | 85.11 | chloroplast | 660 |
TcMADS19 | TCM_007713 | 7.74 | 27,574.3 | 233 | 66.54 | 80.73 | chloroplast | 702 |
TcMADS20 | TCM_007787 | 9.12 | 36,022.57 | 310 | 46.31 | 92.13 | nucleus | 933 |
TcMADS21 | TCM_008703 | 8.5 | 29,428.29 | 258 | 46.99 | 82.79 | nucleus | 777 |
TcMADS22 | TCM_008716 | 5.92 | 22,921.21 | 199 | 56.26 | 89.65 | nucleus | 600 |
TcMADS23 | TCM_008973 | 9.39 | 8995.45 | 78 | 51.89 | 96.15 | chloroplast | 237 |
TcMADS24 | TCM_011475 | 8.97 | 28,016.08 | 241 | 57.36 | 80.17 | nucleus | 726 |
TcMADS25 | TCM_011478 | 6.61 | 27,447.96 | 240 | 58.38 | 73.62 | nucleus | 723 |
TcMADS26 | TCM_011687 | 6.33 | 39,385.48 | 351 | 47.73 | 78.66 | nucleus | 1056 |
TcMADS27 | TCM_012489 | 6.85 | 23,710.15 | 210 | 40.52 | 71.57 | nucleus | 633 |
TcMADS28 | TCM_014051 | 6.13 | 41,766.39 | 370 | 51.46 | 77.22 | chloroplast | 1113 |
TcMADS29 | TCM_014337 | 8.79 | 46,247.61 | 407 | 52.14 | 88.87 | nucleus | 1224 |
TcMADS30 | TCM_014345 | 9.06 | 27,737.47 | 239 | 50.17 | 76.78 | nucleus | 720 |
TcMADS31 | TCM_014661 | 9.83 | 24,429.07 | 210 | 55.07 | 86.33 | chloroplast | 633 |
TcMADS32 | TCM_015044 | 8.82 | 27,249.02 | 236 | 53.76 | 86.78 | nucleus | 711 |
TcMADS33 | TCM_015049 | 9.88 | 27,106.38 | 237 | 47.23 | 90.13 | chloroplast | 714 |
TcMADS34 | TCM_015674 | 5.47 | 27,657.45 | 238 | 69.7 | 87.65 | nucleus | 717 |
TcMADS35 | TCM_016147 | 9.24 | 24,830.39 | 215 | 63.31 | 73.95 | nucleus | 648 |
TcMADS36 | TCM_017242 | 8.51 | 24,320.82 | 209 | 47.08 | 86.75 | nucleus | 630 |
TcMADS37 | TCM_018979 | 9.07 | 27,740.63 | 243 | 34.06 | 85.14 | nucleus | 732 |
TcMADS38 | TCM_018981 | 8.77 | 28,366.14 | 248 | 62.86 | 80.24 | nucleus | 747 |
TcMADS39 | TCM_019362 | 8.23 | 30,811.58 | 267 | 58.24 | 70.15 | nucleus | 804 |
TcMADS40 | TCM_021050 | 9.7 | 17,902.07 | 155 | 45.29 | 89.94 | chloroplast | 468 |
TcMADS41 | TCM_022993 | 9.51 | 40,637.63 | 356 | 53.16 | 76.71 | chloroplast | 1071 |
TcMADS42 | TCM_023006 | 9.2 | 38,815.19 | 354 | 58.36 | 70.54 | nucleus | 1065 |
TcMADS43 | TCM_023041 | 8.93 | 38,451.37 | 354 | 59.01 | 69.49 | nucleus | 1065 |
TcMADS44 | TCM_024579 | 6.04 | 28,901.4 | 252 | 61.39 | 85.48 | nucleus | 759 |
TcMADS45 | TCM_025670 | 8.86 | 26,594.65 | 233 | 64.66 | 74.12 | chloroplast | 702 |
TcMADS46 | TCM_025671 | 9.37 | 26,384.43 | 233 | 63.02 | 70.39 | nucleus | 702 |
TcMADS47 | TCM_025674 | 9.64 | 16,948.73 | 150 | 36.03 | 79.4 | nucleus | 453 |
TcMADS48 | TCM_025676 | 10.29 | 11,744.9 | 103 | 56.26 | 68.25 | chloroplast | 312 |
TcMADS49 | TCM_026842 | 9.26 | 30,499 | 273 | 46.06 | 71.87 | nucleus | 822 |
TcMADS50 | TCM_026845 | 9.47 | 23,787.52 | 207 | 49.15 | 78.74 | chloroplast | 624 |
TcMADS51 | TCM_029234 | 4.91 | 19,812.05 | 174 | 42.71 | 76.21 | nucleus | 525 |
TcMADS52 | TCM_029518 | 9.52 | 20,156.2 | 182 | 44.45 | 79.84 | chloroplast | 549 |
TcMADS53 | TCM_029519 | 9.64 | 49,499.24 | 437 | 50.15 | 68.56 | nucleus | 1314 |
TcMADS54 | TCM_029596 | 9.68 | 34,012.76 | 294 | 66.03 | 74.05 | nucleus | 885 |
TcMADS55 | TCM_032402 | 9.25 | 13,764.45 | 132 | 34.38 | 60.68 | nucleus | 399 |
TcMADS56 | TCM_032403 | 7.74 | 19,620.34 | 172 | 50.98 | 74.24 | chloroplast | 519 |
TcMADS57 | TCM_034148 | 9.08 | 26,051.7 | 225 | 33.21 | 88.36 | chloroplast | 678 |
TcMADS58 | TCM_034501 | 7.64 | 25,504.16 | 227 | 55.81 | 91.06 | nucleus | 684 |
TcMADS59 | TCM_034549 | 9.62 | 21,512.84 | 184 | 50.3 | 88.42 | chloroplast | 555 |
TcMADS60 | TCM_034757 | 5.45 | 37,593.54 | 333 | 59.52 | 84.83 | nucleus | 1002 |
TcMADS61 | TCM_034970 | 5.26 | 38,476.16 | 337 | 60.18 | 82.43 | nucleus | 1014 |
TcMADS62 | TCM_035212 | 8.87 | 24,432.87 | 209 | 61.75 | 78.42 | nucleus | 630 |
TcMADS63 | TCM_036473 | 9.34 | 18,742.04 | 162 | 41.19 | 99.38 | chloroplast | 489 |
TcMADS64 | TCM_036541 | 9.43 | 25,550.24 | 222 | 61.61 | 91.4 | chloroplast | 669 |
TcMADS65 | TCM_036568 | 9.52 | 23,170.78 | 203 | 56.62 | 87 | nucleus | 612 |
TcMADS66 | TCM_037394 | 9.62 | 21,551.01 | 186 | 42.9 | 92.31 | chloroplast | 561 |
TcMADS67 | TCM_040735 | 9.76 | 24,088.7 | 214 | 39.18 | 87.01 | chloroplast | 645 |
TcMADS68 | TCM_042799 | 4.84 | 26,046.39 | 233 | 57.5 | 68.28 | nucleus | 702 |
TcMADS69 | TCM_042848 | 4.81 | 26,121.69 | 233 | 55.41 | 75.41 | nucleus | 702 |
Tandem Duplicated Gene Pairs | Chromosome | Ka | Ks | Ka/Ks |
---|---|---|---|---|
TcMADS43&TcMADS42 | ChrV | 0.108301 | 0.103758 | 1.04379 |
TcMADS43&TcMADS41 | ChrV | 0.213254 | 0.170408 | 1.25143 |
TcMADS42&TcMADS41 | ChrV | 0.215878 | 0.236528 | 0.912695 |
TcMADS49&TcMADS50 | ChrV | 0.098915 | 0.237876 | 0.415826 |
TcMADS45&TcMADS46 | ChrV | 0.078058 | 0.111367 | 0.700902 |
TcMADS68&TcMADS69 | ChrII | 0.035449 | 0.086453 | 0.410042 |
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Zhang, Q.; Hou, S.; Sun, Z.; Chen, J.; Meng, J.; Liang, D.; Wu, R.; Guo, Y. Genome-Wide Identification and Analysis of the MADS-Box Gene Family in Theobroma cacao. Genes 2021, 12, 1799. https://doi.org/10.3390/genes12111799
Zhang Q, Hou S, Sun Z, Chen J, Meng J, Liang D, Wu R, Guo Y. Genome-Wide Identification and Analysis of the MADS-Box Gene Family in Theobroma cacao. Genes. 2021; 12(11):1799. https://doi.org/10.3390/genes12111799
Chicago/Turabian StyleZhang, Qianqian, Sijia Hou, Zhenmei Sun, Jing Chen, Jianqiao Meng, Dan Liang, Rongling Wu, and Yunqian Guo. 2021. "Genome-Wide Identification and Analysis of the MADS-Box Gene Family in Theobroma cacao" Genes 12, no. 11: 1799. https://doi.org/10.3390/genes12111799
APA StyleZhang, Q., Hou, S., Sun, Z., Chen, J., Meng, J., Liang, D., Wu, R., & Guo, Y. (2021). Genome-Wide Identification and Analysis of the MADS-Box Gene Family in Theobroma cacao. Genes, 12(11), 1799. https://doi.org/10.3390/genes12111799