Genome-Wide Identification, Expression Analysis, and Subcellular Localization of Carthamus tinctorius bHLH Transcription Factors
Abstract
:1. Introduction
2. Results and Discussion
2.1. Genome-Wide Identification and Phylogenetic Analysis of Safflower bHLH Genes
2.2. Phylogenetic Analysis
2.3. Motifs and Multiple Sequence Alignment of bHLH Proteins
2.4. Gene Expression Analysis
2.5. Gene Ontology Annotations
2.6. Protein Clustering Networks
2.7. Topology of Conserved Cis-Elements within the Promoter Regions of CtbHLH Genes
2.8. Subcellular Localization of CmbHLH40
3. Materials and Methods
3.1. Plant Materials
3.2. Identification of Safflower bHLH Superfamily Genes
3.3. Motif Elicitation and Phylogenetic Analysis of bHLH Proteins
3.4. Gene Ontology Annotation
3.5. Expression Analysis of the Carthamus bHLH Protein Superfamily
3.6. Protein Interaction Network Prediction and Functional Annotations Using STRING
3.7. Promoter Sequence Analysis of CtbHLH
3.8. Subcellular Localization of CtbHLH40
3.9. Statistical Analysis
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
TFs | Transcription factors |
bHLH | Basic helix–loop–helix |
CLA | Conjugated linoleic acid |
GRAVY | Grand average of hydropathicity |
PI | Isoelectric points |
Kda | Killi dalton |
CDS | Coding sequences |
HMM | Hidden Markov model |
qRT-PCR | Quantitative real-time PCR |
MW | Molecular weight |
TSS | Transcription start site |
GDB | Genome database |
CDD | Conserved Domain |
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Gene Name | Gene ID | Protein Length | PI | MW (Da) | Subcellular Localization | Instability Index | Arabidopsis Homology | GRAVY |
---|---|---|---|---|---|---|---|---|
CtbHLH01(4) | CCG019410.2 | 271 | 7.84 | 29436.75 | Nuclear | 59.80 | AT5G62610.1 | −0.732 |
CtbHLH02(8) | CCG019793.1 | 488 | 6.85 | 54381.40 | Nuclear | 51.53 | AT4G16430.1 | −0.542 |
CtbHLH03(2) | CCG020831.1 | 314 | 7.78 | 35586.93 | Nuclear | 46.88 | AT1G30670.1 | −0.770 |
CtbHLH04(14) | CCG021763.1 | 264 | 6.66 | 29051.21 | Nuclear | 43.29 | AT4G09180.1 | −0.272 |
CtbHLH05(11) | CCG022142.1 | 424 | 5.63 | 46461.98 | Nuclear | 61.08 | AT3G20640.1 | −0.770 |
CtbHLH06(9) | CCG023511.1 | 396 | 5.54 | 45156.48 | Nuclear | 43.12 | AT2G31210.1 | −0.620 |
CtbHLH07(7) | CCG028074.4 | 480 | 6.73 | 53210.85 | Nuclear | 48.98 | AT1G27660.1 | −0.476 |
CtbHLH08(9) | CCG028576.1 | 426 | 5.62 | 47924.37 | Nuclear | 37.73 | AT1G06170.1 | −0.654 |
CtbHLH09(7) | CCG029033.2 | 420 | 9.34 | 48353.34 | Nuclear | 51.47 | AT3G23210.1 | −0.712 |
CtbHLH10 | CCG029306.2 | 294 | 5.93 | 32779.18 | Nuclear | 67.22 | AT3G19860.2 | −1.017 |
CtbHLH11(12) | CCG031433.1 | 373 | 5.88 | 38966.22 | Nuclear | 56.54 | AT2G24260.1 | −0.424 |
CtbHLH12(9) | CCG031433.1 | 313 | 6.64 | 34357.55 | Nuclear | 57.98 | AT1G68810.1 | −0.587 |
CtbHLH13(14) | CCG003415.1 | 398 | 5.61 | 44597.03 | Nuclear | 61.12 | AT2G42280.1 | −0.826 |
CtbHLH14(7) | CCG003696.1 | 362 | 6.53 | 39563.23 | Nuclear | 67.71 | AT1G51140.1 | −0.690 |
CtbHLH15(11) | CCG004828.1 | 363 | 6.33 | 39459.94 | Nuclear | 57.93 | AT1G61660.1 | −0.602 |
CtbHLH16(5) | CCG006936.1 | 320 | 5.21 | 35518.73 | Nuclear | 60.39 | AT3G57800.1 | −0.585 |
CtbHLH17(1) | CCG009097.1 | 513 | 5.61 | 56099.86 | Nuclear | 42.63 | AT3G07340.1 | −0.677 |
CtbHLH18(9) | CCG010966.1 | 249 | 9.15 | 27766.58 | Nuclear | 31.23 | AT1G68810.1 | −0.453 |
CtbHLH19(10) | CCG015095.1 | 437 | 7.81 | 49777.63 | Nuclear | 34.05 | AT1G10610.1 | −0.390 |
CtbHLH20(14) | CCG016487.1 | 388 | 5.95 | 43102.83 | Nuclear | 58.48 | AT2G42280.1 | −0.726 |
CtbHLH21(1) | CCG030113.1 | 474 | 6.34 | 51930.85 | Nuclear | 51.00 | AT3G07340.1 | −0.720 |
CtbHLH22(14) | CCG000235.1 | 401 | 6.07 | 44439.58 | Nuclear | 69.25 | AT1G51140.1 | −0.913 |
CtbHLH23(7) | CCG000365.1 | 283 | 5.59 | 31696.50 | Nuclear | 52.80 | AT2G14760.3 | −0.654 |
CtbHLH24(9) | CCG001914.1 | 312 | 7.05 | 34294.77 | Nuclear | 64.73 | AT1G72210.1 | −0.500 |
CtbHLH25(10) | CCG002853.1 | 414 | 7.96 | 46510.11 | Nuclear | 41.81 | AT1G10610.1 | −0.434 |
CtbHLH26(2) | CCG003971.1 | 353 | 6.47 | 39567.82 | Nuclear | 40.90 | AT1G10120.1 | −0.587 |
CtbHLH27(9) | CCG006284.1 | 375 | 6.37 | 42123.27 | Nuclear | 69.08 | AT1G68810.1 | −0.696 |
CtbHLH28(8) | CCG006712.1 | 488 | 6.85 | 54381.40 | Nuclear | 52.40 | AT4G16430.1 | −0.548 |
CtbHLH29(14) | CCG008781.1 | 428 | 6.63 | 48008.56 | Nuclear | 61.50 | AT2G42280.1 | −0.997 |
CtbHLH30(2) | CCG009709.1 | 364 | 8.13 | 40547.38 | Nuclear | 43.90 | AT3G23690.1 | −0.736 |
CtbHLH31(3) | CCG010368.1 | 544 | 5.42 | 58619.71 | Nuclear | 57.98 | AT1G68920.1 | −0.712 |
CtbHLH32(6) | CCG011082.1 | 706 | 5.95 | 77127.87 | Nuclear | 58.02 | AT2G20180.2 | −0.576 |
CtbHLH33(9) | CCG011764.1 | 336 | 7.72 | 37338.69 | Nuclear | 47.03 | AT4G37850.1 | −0.424 |
CtbHLH34(7) | CCG013712.2 | 250 | 5.64 | 27865.55 | Nuclear | 59.41 | AT5G54680.1 | −0.614 |
CtbHLH35(13) | CCG014470.1 | 382 | 5.35 | 39191.40 | Nuclear | 53.49 | AT4G30980.1 | −0.375 |
CtbHLH36(2) | CCG017266.1 | 376 | 5.46 | 42211.90 | Nuclear | 49.28 | AT1G68920.1 | −0.779 |
CtbHLH37(15) | CCG018780.1 | 186 | 7.03 | 21187.15 | Nuclear | 44.33 | AT4G20970.1 | −0.465 |
CtbHLH38(1) | CCG018923.1 | 460 | 6.68 | 50715.86 | Nuclear | 56.68 | AT3G07340.1 | −0.676 |
CtbHLH39(8) | CCG018976.1 | 617 | 9.04 | 69705.26 | Nuclear | 53.97 | AT2G46510.1 | −0.497 |
CtbHLH40(1) | CCG019036.1 | 519 | 6.31 | 57019.01 | Nuclear | 44.67 | AT3G07340.1 | −0.682 |
CtbHLH41(4) | CCG019190.1 | 298 | 5.67 | 32673.94 | Nuclear | 64.80 | AT3G57800.1 | −0.933 |
CtbHLH01(4) | CCG019410.2 | 271 | 7.84 | 29436.75 | Nuclear | 59.80 | AT5G62610.1 | −0.732 |
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Hong, Y.; Ahmad, N.; Tian, Y.; Liu, J.; Wang, L.; Wang, G.; Liu, X.; Dong, Y.; Wang, F.; Liu, W.; et al. Genome-Wide Identification, Expression Analysis, and Subcellular Localization of Carthamus tinctorius bHLH Transcription Factors. Int. J. Mol. Sci. 2019, 20, 3044. https://doi.org/10.3390/ijms20123044
Hong Y, Ahmad N, Tian Y, Liu J, Wang L, Wang G, Liu X, Dong Y, Wang F, Liu W, et al. Genome-Wide Identification, Expression Analysis, and Subcellular Localization of Carthamus tinctorius bHLH Transcription Factors. International Journal of Molecular Sciences. 2019; 20(12):3044. https://doi.org/10.3390/ijms20123044
Chicago/Turabian StyleHong, Yingqi, Naveed Ahmad, Yuanyuan Tian, Jianyu Liu, Liyan Wang, Gang Wang, Xiuming Liu, Yuanyuan Dong, Fawei Wang, Weican Liu, and et al. 2019. "Genome-Wide Identification, Expression Analysis, and Subcellular Localization of Carthamus tinctorius bHLH Transcription Factors" International Journal of Molecular Sciences 20, no. 12: 3044. https://doi.org/10.3390/ijms20123044