Systematic Investigation of TCP Gene Family: Genome-Wide Identification and Light-Regulated Gene Expression Analysis in Pepino (Solanum Muricatum)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Identification, Basic Characterization and Chromosome Location of SmTCPs
2.2. Phylogenetic Analysis of SmTCPs
2.3. Conserved Motifs and Gene Structure Analysis
2.4. Promoter Region Cis-Acting Element Analysis
2.5. Data mining of A. thaliana Gene Regulatory Network
2.6. RNA Extraction and Transcriptome Sequencing
2.7. Expression Analysis of SmTCP Genes and Accurate Amplification of Candidate Reference Genes
3. Results
3.1. Identification, Chromosomal Location, and Classification of TCP Family Members in S. muricatum
3.2. Taxonomic Classification and Phylogenetic Analysis of SmTCPs Genes
3.3. Structural and Conserved Sequence Analyses of SmTCPs
3.4. Chromosome Distribution of SmTCPs
3.5. Gene Duplication Analysis and Collinear Analysis
3.6. Response of SmTCPs Expression with Different Light Treatments
3.7. Effect of Red and Blue Light on Differential Expression Genes in S. muricatum
3.8. Interaction Network of S. muricatum DETCPs
3.9. Response of AtTCP Expression with Different Light Treatment and Co-expression Analysis
3.10. Comparative Analysis of TCP Regulatory Genes Annotation between ARABIDOPSIS and S. muricatum
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Gene ID | TCP Number | Chromosome Location | Amino Acid | Molecular Weight (Da) | Isoelectric Point |
---|---|---|---|---|---|
Smu01G002900.1 | SmTCP1 | Chr01:3332723-3335734 | 258 | 26,738.7 | 9.25 |
Smu01G010770.1 | SmTCP2 | Chr01:27066460-27067813 | 183 | 21,100.8 | 10.14 |
Smu01G010850.1 | SmTCP3 | Chr01:27800921-27803184 | 307 | 35,322.1 | 10.71 |
Smu01G012690.1 | SmTCP4 | Chr01:43848293-43848790 | 165 | 19,012.3 | 10.38 |
Smu01G028040.1 | SmTCP5 | Chr01:98110326-98111135 | 269 | 29,026.1 | 11 |
Smu01G037260.1 | SmTCP6 | Chr01:105533447-105536012 | 541 | 58,109.5 | 7.42 |
Smu02G012810.1 | SmTCP7 | Chr02:54705676-54706978 | 236 | 26,613 | 9.71 |
Smu02G014130.1 | SmTCP8 | Chr02:55729354-55730193 | 279 | 30,015.3 | 8.73 |
Smu02G019380.1 | SmTCP9 | Chr02:60587194-60588180 | 328 | 37,236.6 | 5.24 |
Smu02G031600.1 | SmTCP10 | Chr02:70759903-70761444 | 300 | 33,948.8 | 8.87 |
Smu02G032390.1 | SmTCP11 | Chr02:71403226-71405184 | 292 | 32,605.8 | 7.17 |
Smu03G006140.1 | SmTCP12 | Chr03:13497696-13498193 | 165 | 18,902.3 | 10.51 |
Smu03G006260.1 | SmTCP13 | Chr03:14258604-14259658 | 218 | 25,333.8 | 11.22 |
Smu03G006480.1 | SmTCP14 | Chr03:16602979-16603476 | 165 | 18,863.3 | 10.54 |
Smu03G016390.1 | SmTCP15 | Chr03:68102671-68103432 | 253 | 27,101.6 | 8.47 |
Smu03G016550.1 | SmTCP16 | Chr03:68342489-68343592 | 367 | 38,983.3 | 4.82 |
Smu03G026310.1 | SmTCP17 | Chr03:76801657-76802652 | 331 | 37,555.6 | 6.08 |
Smu03G027550.1 | SmTCP18 | Chr03:77806134-77807784 | 406 | 42,963.9 | 7.47 |
Smu03G030930.1 | SmTCP19 | Chr03:80379818-80380979 | 351 | 39,923.1 | 9.4 |
Smu04G003880.1 | SmTCP20 | Chr04:4042925 -4046662 | 268 | 28,082.3 | 10.39 |
Smu04G011520.1 | SmTCP21 | Chr04:28185097-28186262 | 229 | 26,440.1 | 11.03 |
Smu04G012560.1 | SmTCP22 | Chr04:38220364-38221776 | 241 | 27,598.3 | 10.75 |
Smu05G000850.1 | SmTCP23 | Chr05:593333-594403 | 356 | 40,793.1 | 9.44 |
Smu05G003500.1 | SmTCP24 | Chr05:3280292-3281413 | 373 | 41,513.7 | 6.95 |
Smu06G021110.1 | SmTCP25 | Chr06:66811270-66812244 | 324 | 34,685 | 7.47 |
Smu06G024960.1 | SmTCP26 | Chr06:69716855-69718816 | 372 | 41,736.1 | 7.93 |
Smu06G025220.1 | SmTCP27 | Chr06:69948309-69949232 | 307 | 34,126.2 | 9.47 |
Smu06G025710.1 | SmTCP28 | Chr06:70332967-70334440 | 395 | 43,032.7 | 6.77 |
Smu07G018850.1 | SmTCP29 | Chr07:76470532-76471467 | 311 | 35,168.5 | 7.06 |
Smu07G021660.1 | SmTCP30 | Chr07:78741136-78742329 | 397 | 43,287.3 | 6.77 |
Smu08G005820.1 | SmTCP31 | Chr08:7958152-7965853 | 393 | 43,909.8 | 6.76 |
Smu08G005850.1 | SmTCP32 | Chr08:8116621-8122423 | 392 | 43,764.5 | 6.2 |
Smu08G008280.1 | SmTCP33 | Chr08:30519308-30519805 | 165 | 18,777.1 | 10.39 |
Smu08G008340.1 | SmTCP34 | Chr08:30990318-30991540 | 275 | 31,489.4 | 10.2 |
Smu08G008390.1 | SmTCP35 | Chr08:31805011-31806191 | 272 | 31,258.4 | 10.6 |
Smu08G023240.1 | SmTCP36 | Chr08:80179377-80180495 | 372 | 39,709.2 | 7.28 |
Smu09G005030.1 | SmTCP37 | Chr09:6222598-6223693 | 201 | 21,337 | 8.5 |
Smu10G003890.1 | SmTCP38 | Chr10:3619195-3620871 | 558 | 63,952.9 | 7.1 |
Smu11G014110.1 | SmTCP39 | Chr11:17567466-17569182 | 395 | 42,372.6 | 8.57 |
Smu12G003120.1 | SmTCP40 | Chr12:2972387-2973937 | 516 | 57,154.9 | 7.53 |
Smuptg000412lG000050.1 | SmTCP41 | ptg000412l:62921-64509 | 381 | 43,577.7 | 8.68 |
SmTCP | Classification | B_fpkm | F_fpkm | R_fpkm | P-Value | FDR | Homologous Genes | Homologous Encoding Genes |
---|---|---|---|---|---|---|---|---|
SmTCP19 | CYC/TBI | 3.84 | 4.04 | 4.51 | 3.11 × 10−8 | 1.92 × 10−7 | SlTCP9 | Solyc03g119770.3.1 |
SmTCP26 | CYC/TBI | 11.30 | 15.28 | 16.16 | 8.65 × 10−28 | 1.65 × 10−26 | SlTCP8 | Solyc06g069240.2.1 |
SmTCP23 | CYC/TBI | 1.52 | 2.27 | 2.65 | 0.00249590 | 0.008556416 | ATTCP12 | AT1G68800 |
SmTCP40 | CIN | 0.58 | 0.23 | 0.41 | 9.74 × 10−5 | 0.000387219 | ATTCP4 | AT3G15030 |
SmTCP11 | CIN | 1.80 | 0.86 | 1.01 | 0.00666871 | 0.025969579 | SlTCP5 | Solyc02g089020.2.1 |
SmTCP24 | Class I | 6.07 | 6.13 | 8.64 | 1.1 × 10−13 | 1.90 × 10−12 | ATTCP15 | At1G69690 |
SmTCP16 | Class I | 1.81 | 1.53 | 1.46 | 0.00027819 | 0.001131583 | SlTCP21/ATTCP19 | Solyc03g006800.1.1/AT5G51910 |
SmTCP28 | Class I | 8.49 | 10.00 | 11.99 | 1.45 × 10−20 | 1.79 × 10−19 | SlTCP16 | Solyc03g116320.3.1 |
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Si, C.; Zhan, D.; Wang, L.; Sun, X.; Zhong, Q.; Yang, S. Systematic Investigation of TCP Gene Family: Genome-Wide Identification and Light-Regulated Gene Expression Analysis in Pepino (Solanum Muricatum). Cells 2023, 12, 1015. https://doi.org/10.3390/cells12071015
Si C, Zhan D, Wang L, Sun X, Zhong Q, Yang S. Systematic Investigation of TCP Gene Family: Genome-Wide Identification and Light-Regulated Gene Expression Analysis in Pepino (Solanum Muricatum). Cells. 2023; 12(7):1015. https://doi.org/10.3390/cells12071015
Chicago/Turabian StyleSi, Cheng, Deli Zhan, Lihui Wang, Xuemei Sun, Qiwen Zhong, and Shipeng Yang. 2023. "Systematic Investigation of TCP Gene Family: Genome-Wide Identification and Light-Regulated Gene Expression Analysis in Pepino (Solanum Muricatum)" Cells 12, no. 7: 1015. https://doi.org/10.3390/cells12071015