Comprehensive Analysis of the GiTCP Gene Family and Its Expression Under UV-B Radiation in Glycyrrhiza inflata Bat
Abstract
:1. Introduction
2. Results
2.1. Identification and Physicochemical Properties of Members of the GiTCP Gene Family of G. inflata
2.2. Phylogenetic Construction, Motif, Domain, and Gene Structure Analysis of the GiTCP Gene Family in G. inflata
2.3. Distribution of GiTCP Genes on Chromosomes and Predictive Analysis of Secondary Structure in G. inflata
2.4. Phylogenetic Tree Analysis of TCP Genes
2.5. Cis-Acting Element Analysis of GiTCP Genes in G. inflata
2.6. Protein Interaction Network Analysis of GiTCPs
2.7. GO Functional Annotation of GiTCP Genes in G. inflata
2.8. Effect of UV-B Radiation on G. inflata
2.9. Subcellular Localization Analysis
2.10. Expression Pattern Analysis of GiTCP Genes in Licorice Under UV-B Radiation
3. Discussion
4. Materials and Methods
4.1. Plant Materials, Growth Conditions, and Treatments
4.2. Identification of TCP Gene Family Members in Licorice
4.3. Domain, Gene Structure, and Conserved Motifs of TCP Proteins in Licorice
4.4. Chromosomal Mapping and Secondary Structure Analysis of TCP Genes in Licorice
4.5. Phylogenetic Tree Analysis of TCP Genes in Licorice
4.6. Analysis of Cis-Acting Elements of TCP Gene Family in G. inflata
4.7. Construction of TCP Protein Interaction Network in G. inflata
4.8. Subcellular Localization Assays
4.9. Transcriptome Sequencing Analysis
4.10. GO Analysis of TCP Genes in Licorice
4.11. RNA Isolation and qRT-PCR
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
TCP | teosinte branched 1/cincinnata/proliferating cell factor |
TB1 | teosinte branched 1 |
PCF | proliferating cell factor |
CYC | cycloidea |
Ms | Medicago sativa L |
Ma | Musa acuminata |
Pg | Panax ginseng |
Ap | Andrographis paniculata |
Dch | Dendrobium |
Gi | G. inflata Bat |
GA3 | gibberellic acid 3 |
MeJA | methyl jasmonate |
bZIP | basic region/leucine zipper |
AA | amino acid sequence length |
MW | molecular weight |
pI | isoelectric point |
GRAVY | grand average of hydropathicity |
II | instability index |
AI | aliphatic index |
SL | subcellular localization |
N | nucleus |
C | cytoplasm |
CP | chloroplast |
E | extracellular matrix |
M | mitochondria |
Pm | plasma membrane |
At | Arabidopsis thaliana |
Eu | Eucommia ulmoides |
GO | gene ontology |
qRT-PCR | quantitative real-time PCR |
UV-B | ultraviolet B |
Cr | Catharanthus roseus |
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Gene Name | Sequence ID | AA | MW | pI | II | AI | GRAVY | SL |
---|---|---|---|---|---|---|---|---|
GiTCP1 | Glyur000008s00001296.1 | 433 | 48,419.6 | 6.35 | 56.22 | 58 | −0.688 | N,C |
GiTCP2 | Glyur000014s00002559.1 | 424 | 46,637.73 | 6.56 | 55.14 | 60 | −0.806 | N,C,CP |
GiTCP3 | Glyur000020s00001802.1 | 426 | 46,357.61 | 6.39 | 57.12 | 53 | −0.877 | N,C |
GiTCP4 | Glyur000039s00004191.1 | 378 | 42,805.57 | 6.46 | 55.23 | 46 | −1.098 | N,C |
GiTCP5 | Glyur000050s00005694.1 | 369 | 40,912.51 | 8.97 | 59.19 | 62 | −0.729 | N,C,E |
GiTCP6 | Glyur000073s00007830.1 | 421 | 45,416.08 | 7.41 | 70.02 | 58 | −0.769 | N,C |
GiTCP7 | Glyur000175s00012061.1 | 375 | 39,457.06 | 6.26 | 47.75 | 62 | −0.461 | N |
GiTCP8 | Glyur000192s00009341.1 | 507 | 54,268.62 | 7.26 | 60.82 | 58 | −0.736 | N |
GiTCP9 | Glyur000208s00014261.1 | 357 | 39,483.73 | 6.17 | 66.29 | 59 | −0.815 | N |
GiTCP10 | Glyur000275s00017056.1 | 406 | 44,812.15 | 9.32 | 54.38 | 67 | −0.623 | N,C,E |
GiTCP11 | Glyur000278s00017293.1 | 524 | 57,436.66 | 7.42 | 52.22 | 61 | −0.736 | N,CP |
GiTCP12 | Glyur000329s00019843.1 | 429 | 46,829.39 | 6.33 | 41.64 | 64 | −0.559 | N,CP,M |
GiTCP13 | Glyur000418s00021337.1 | 372 | 41,089.66 | 7.13 | 53.33 | 69 | −0.617 | N,CP |
GiTCP14 | Glyur000513s00025388.1 | 420 | 43,972.18 | 6.42 | 55.38 | 57 | −0.606 | N |
GiTCP15 | Glyur000523s00021974.1 | 429 | 48,570.05 | 7.31 | 51.61 | 57 | −0.943 | N,Pm |
GiTCP16 | Glyur000529s00019352.1 | 380 | 40,865.72 | 6.15 | 53.77 | 61 | −0.611 | N,CP,M |
GiTCP17 | Glyur000594s00025967.1 | 490 | 54,254.93 | 6.68 | 58.91 | 51 | −1.027 | N,CP |
GiTCP18 | Glyur000643s00026942.1 | 392 | 43,118.88 | 7.91 | 52.49 | 67 | −0.754 | N,C,CP |
GiTCP19 | Glyur000658s00024843.1 | 209 | 22,115.54 | 8.46 | 63.38 | 70 | −0.266 | N,C,M |
GiTCP20 | Glyur000815s00035011.1 | 512 | 57,147.71 | 9.42 | 55.92 | 57 | −0.972 | N |
GiTCP21 | Glyur001815s00041763.1 | 378 | 42,273.69 | 9.2 | 56.38 | 72 | −0.598 | N,CP |
GiTCP22 | Glyur002854s00044943.1 | 329 | 34,959.7 | 9.01 | 51.47 | 66 | −0.751 | N,CP,E |
GiTCP23 | Glyur002883s00039141.1 | 343 | 36,224.26 | 9.72 | 62.61 | 73 | −0.334 | N,Pm |
GiTCP24 | Glyur007388s00045515.1 | 256 | 27,486.88 | 9.38 | 54.13 | 68 | −0.627 | N,CP,M |
Gene Name | Sequence ID | Alpha Helix | Extended Strand | Beta Turn | Random Coil |
---|---|---|---|---|---|
GiTCP1 | Glyur000008s00001296.1 | 27.25% | 12.24% | 1.85% | 58.66% |
GiTCP2 | Glyur000014s00002559.1 | 19.81% | 11.56% | 3.77% | 64.86% |
GiTCP3 | Glyur000020s00001802.1 | 15.49% | 12.44% | 3.99% | 68.08% |
GiTCP4 | Glyur000039s00004191.1 | 33.07% | 8.73% | 2.38% | 55.82% |
GiTCP5 | Glyur000050s00005694.1 | 15.18% | 13.28% | 3.25% | 68.29% |
GiTCP6 | Glyur000073s00007830.1 | 20.67% | 11.88% | 4.75% | 62.71% |
GiTCP7 | Glyur000175s00012061.1 | 12.53% | 12.80% | 3.47% | 71.02% |
GiTCP8 | Glyur000192s00009341.1 | 19.13% | 10.65% | 3.35% | 66.86% |
GiTCP9 | Glyur000208s00014261.1 | 14.85% | 12.32% | 3.08% | 69.75% |
GiTCP10 | Glyur000275s00017056.1 | 18.72% | 13.05% | 5.42% | 62.81% |
GiTCP11 | Glyur000278s00017293.1 | 28.05% | 11.64% | 3.63% | 56.68% |
GiTCP12 | Glyur000329s00019843.1 | 22.38% | 14.22% | 3.03% | 60.37% |
GiTCP13 | Glyur000418s00021337.1 | 18.82% | 7.80% | 3.49% | 69.89% |
GiTCP14 | Glyur000513s00025388.1 | 22.14% | 11.90% | 3.57% | 62.71% |
GiTCP15 | Glyur000523s00021974.1 | 36.60% | 6.76% | 2.33% | 54.31% |
GiTCP16 | Glyur000529s00019352.1 | 14.47% | 11.84% | 3.42% | 70.28% |
GiTCP17 | Glyur000594s00025967.1 | 25.21% | 14.17% | 7.5% | 53.12% |
GiTCP18 | Glyur000643s00026942.1 | 13.27% | 13.52% | 4.59% | 68.62% |
GiTCP19 | Glyur000658s00024843.1 | 19.62% | 20.57% | 2.87% | 56.94% |
GiTCP20 | Glyur000815s00035011.1 | 20.70% | 15.23% | 4.10% | 59.96% |
GiTCP21 | Glyur001815s00041763.1 | 38.89% | 12.70% | 5.29% | 43.12% |
GiTCP22 | Glyur002854s00044943.1 | 23.40% | 8.81% | 6.08% | 61.70% |
GiTCP23 | Glyur002883s00039141.1 | 20.41% | 16.62% | 4.66% | 58.31% |
GiTCP24 | Glyur007388s00045515.1 | 25.0% | 16.80% | 3.12% | 55.08% |
Class | GO Term | Annotation | GiTCP Genes |
---|---|---|---|
MF | GO:0005488 | Binding | GiTCP1, GiTCP14, GiTCP16, GiTCP19, GiTCP23 |
GO:0140110 | Transcription regulator activity | GiTCP14, GiTCP16, GiTCP19, GiTCP23, GiTCP24 | |
CC | GO:0032991 | Protein-containing complex | GiTCP24 |
GO:0110165 | Cellular anatomical entity | GiTCP14, GiTCP16, GiTCP19, GiTCP23, GiTCP24 | |
BP | GO:0000003 | Reproduction | GiTCP14 |
GO:0008152 | Metabolic process | GiTCP1, GiTCP14, GiTCP16, GiTCP19, GiTCP23, GiTCP24 | |
GO:0009987 | Cellular process | GiTCP1, GiTCP14, GiTCP16, GiTCP19, GiTCP23, GiTCP24 | |
GO:0022414 | Reproductive process | GiTCP14 | |
GO:0032501 | Multicellular organismal process | GiTCP14, GiTCP19, GiTCP23 | |
GO:0032502 | Developmental process | GiTCP14, GiTCP19, GiTCP23 | |
GO:0048511 | Rhythmic process | GiTCP14, GiTCP19 | |
GO:0048519 | Negative regulation of biological process | GiTCP23 | |
GO:0050789 | Regulation of biological process | GiTCP14, GiTCP16, GiTCP19, GiTCP23 | |
GO:0050896 | Response to stimulus | GiTCP14, GiTCP16 | |
GO:0065007 | Biological regulation | GiTCP14, GiTCP16, GiTCP19, GiTCP23 |
Gene Name | Forward Primer (5′-3′) | Reverse Primer (5′-3′) |
GiTCP3 | CAAACTCCTCGTCAACCCGA | CTTTGTGTGCCGGTCCTTTG |
GiTCP6 | CCGAATTAGCCGCGAACAAG | GAGCTCACGTGTCAGTTGGA |
GiTCP7 | GCAGCGACGAGTATTCCAGA | CGCTGGAACTAACACTGGGT |
GiTCP8 | TCTACCAGCCCTCTCAGCAT | GATCGGAATTGTCGGTGGGT |
GiTCP11 | CGTGTCTGGCCTTTTCCGAT | CCCAAATGGTCTTTCCTTGCG |
GiTCP12 | GCTCCTGTTGGGTTTGATGC | AGGGTCCCCCTATGGGAAAA |
GiTCP14 | GCGAGACGATAGAGTGGCTC | CGGAGAAGGTGCTAGGGTTG |
GiTCP17 | GGCACCACCACTCATCAAGA | GCTGTTGTCACTGAGAGCCT |
GiTCP22 | CCTGGTTTGGAACTGGGGTT | GGCCATGCAATTCCACCTTG |
GiTCP23 | TGTTCAGCTCCAACCAGCAA | TGGAAGAAGAGCGCGACAAT |
GiTCP24 | TACCCTCGCGGTGAAGAAAC | GCGGCGATAATTGACGGTTC |
β-actin | CCTCATGCCATCCTTCGTC | TCTTTGCAGTCTCGAGTTCTTG |
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Liu, Z.; Zhao, J.; Xiao, Y.; Li, C.; Miao, R.; Chen, S.; Zhang, D.; Zhou, X.; Li, M. Comprehensive Analysis of the GiTCP Gene Family and Its Expression Under UV-B Radiation in Glycyrrhiza inflata Bat. Int. J. Mol. Sci. 2025, 26, 159. https://doi.org/10.3390/ijms26010159
Liu Z, Zhao J, Xiao Y, Li C, Miao R, Chen S, Zhang D, Zhou X, Li M. Comprehensive Analysis of the GiTCP Gene Family and Its Expression Under UV-B Radiation in Glycyrrhiza inflata Bat. International Journal of Molecular Sciences. 2025; 26(1):159. https://doi.org/10.3390/ijms26010159
Chicago/Turabian StyleLiu, Ziliang, Jiaang Zhao, Ying Xiao, Caijuan Li, Rong Miao, Sijin Chen, Dan Zhang, Xiangyan Zhou, and Mengfei Li. 2025. "Comprehensive Analysis of the GiTCP Gene Family and Its Expression Under UV-B Radiation in Glycyrrhiza inflata Bat" International Journal of Molecular Sciences 26, no. 1: 159. https://doi.org/10.3390/ijms26010159
APA StyleLiu, Z., Zhao, J., Xiao, Y., Li, C., Miao, R., Chen, S., Zhang, D., Zhou, X., & Li, M. (2025). Comprehensive Analysis of the GiTCP Gene Family and Its Expression Under UV-B Radiation in Glycyrrhiza inflata Bat. International Journal of Molecular Sciences, 26(1), 159. https://doi.org/10.3390/ijms26010159