Genome-Wide Identification of the Auxin Response Factor (ARF) Gene Family and Their Expression Analysis during Flower Development of Osmanthus fragrans
Abstract
:1. Introduction
2. Materials and Methods
2.1. Identification of ARF Genes in Osmanthus fragrans
2.2. Analysis of Gene Structures, Conserved Domains and Subcellular Localizations
2.3. Chromosomal Localization, Gene Duplication and Evolution Analysis of OfARF Genes
2.4. Conserved Motifs and Promoter Cis-acting Regulatory DNA Elements Analysis
2.5. Phylogenetic Analysis of OfARF Genes
2.6. Plant Material Collection, RNA extraction and cDNA Synthesis
2.7. Expression Analysis of OfARF Genes
2.8. IAA Content Measurement
3. Results
3.1. Identification of the OfARF Gene Family
3.2. Phylogenetic Analysis and Gene Structure of OfARFs
3.3. Analysis of Conserved Domains of Osmanthus fragrans Auxin Response Factor (OfARF) Proteins
3.4. Motif Characterization and Promoter Analysis of Osmanthus fragrans Auxin Response Factor (OfARF) Proteins
3.5. Subcellular Localization Analysis of OfARFs
3.6. Expression of OfARF Genes in Different Tissues and Various Flower Development Stages of O. fragrans
3.7. Endogenous Indoleacetic Acid (IAA) Concentration Measurement
4. Discussions
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Gene Name | Gene ID | Exon No. a | Len b (aa) | MW c (kDa) | pI d | Instability Index | GRAVY e | Conserved Domain | Homologous |
---|---|---|---|---|---|---|---|---|---|
OfARF1a | Contig151.75 | 4 | 702 | 77.19 | 7.29 | 48.43 | −0.305 | B3, ARF, Aux/IAA | AtARF16 |
OfARF1b | Contig73.170 | 6 | 760 | 83.87 | 7.82 | 46.64 | −0.289 | B3, ARF, Aux/IAA | AtARF16 |
OfARF2 | Contig328.11 | 4 | 685 | 74.8 | 5.81 | 40.99 | −0.305 | B3, ARF, Aux/IAA | AtARF16 |
OfARF3a | Contig281.61 | 4 | 687 | 75.86 | 7.91 | 50.00 | −0.322 | B3, ARF, Aux/IAA | AtARF16 |
OfARF3b | Contig592.12 | 5 | 646 | 71.52 | 6.55 | 46.00 | −0.248 | B3, ARF, Aux/IAA | AtARF16 |
OfARF4a | Contig37.40 | 3 | 674 | 74.86 | 6.43 | 47.95 | −0.370 | B3, ARF, Aux/IAA | AtARF16 |
OfARF4b | Contig295.42 | 2 | 601 | 66.52 | 6.36 | 42.06 | −0.428 | B3, ARF | AtARF16 |
OfARF5a | Contig275.68 | 4 | 704 | 77.28 | 6.48 | 44.24 | −0.283 | B3, ARF, Aux/IAA | AtARF16 |
OfARF5b | Contig10.361 | 3 | 690 | 76.3 | 6.69 | 47.23 | −0.332 | B3, ARF, Aux/IAA | AtARF16 |
OfARF6a | Contig86.172 | 3 | 681 | 75.78 | 6.02 | 48.21 | −0.374 | B3, ARF, Aux/IAA | AtARF16 |
OfARF6b | Contig12.215 | 2 | 677 | 75.43 | 7.25 | 43.42 | −0.407 | B3, ARF, Aux/IAA | AtARF10 |
OfARF7a | Contig84.135 | 2 | 552 | 60.82 | 5.25 | 47.13 | −0.355 | B3, ARF | AtARF17 |
OfARF7b | Contig77.21 | 2 | 552 | 60.85 | 5.95 | 46.36 | −0.281 | B3, ARF | AtARF17 |
OfARF8a | Contig38.67 | 2 | 372 | 42.26 | 6.8 | 41.46 | −0.257 | B3, ARF | AtARF17 |
OfARF8b | Contig38.68 | 2 | 478 | 53.89 | 6.06 | 42.24 | −0.343 | B3, ARF | AtARF17 |
OfARF9a | Contig26.229 | 11 | 692 | 75.99 | 6.33 | 60.34 | −0.451 | B3, ARF | AtARF3 |
OfARF9b | Contig172.11 | 11 | 726 | 79.71 | 6.92 | 48.75 | −0.367 | B3, ARF | AtARF3 |
OfARF10a | Contig151.50 | 13 | 753 | 84.46 | 6.05 | 51.77 | −0.432 | B3, ARF, Aux/IAA | AtARF4 |
OfARF10b | Contig73.186 | 12 | 787 | 87.64 | 5.97 | 48.99 | −0.409 | B3, ARF, Aux/IAA | AtARF4 |
OfARF11a | Contig324.17 | 14 | 659 | 73.98 | 5.84 | 65.97 | −0.551 | B3, ARF, Aux/IAA | AtARF1 |
OfARF11b | Contig97.3 | 14 | 653 | 73.33 | 5.76 | 64.99 | −0.525 | B3, ARF, Aux/IAA | AtARF1 |
OfARF12 | Contig194.92 | 14 | 665 | 74.53 | 6.08 | 61.36 | −0.520 | B3, ARF, Aux/IAA | AtARF1 |
OfARF13 | Contig76.252 | 14 | 842 | 94.36 | 6.28 | 56.97 | −0.568 | B3, ARF, Aux/IAA | AtARF2 |
OfARF14a | Contig6.38 | 14 | 828 | 92.59 | 6.06 | 61.49 | −0.549 | B3, ARF, Aux/IAA | AtARF2 |
OfARF14b | Contig2.130 | 14 | 838 | 93.5 | 6.02 | 64.87 | −0.609 | B3, ARF, Aux/IAA | AtARF2 |
OfARF15 | Contig105.88 | 10 | 332 | 37.46 | 7.26 | 55.57 | −0.436 | B3, ARF | AtARF9 |
OfARF16a | Contig317.63 | 14 | 658 | 74.16 | 6.7 | 57.20 | −0.550 | B3, ARF, Aux/IAA | AtARF9 |
OfARF16b | Contig153.78 | 12 | 411 | 46.67 | 6.77 | 60.92 | −0.372 | B3, ARF | AtARF9 |
OfARF17a | Contig54.9 | 14 | 666 | 74.97 | 6.67 | 56.90 | −0.414 | B3, ARF, Aux/IAA | AtARF9 |
OfARF17b | Contig21.49 | 14 | 634 | 71.54 | 6.33 | 49.95 | −0.476 | B3, ARF, Aux/IAA | AtARF9 |
OfARF18 | Contig354.37 | 15 | 720 | 81.77 | 9.05 | 50.43 | −0.551 | B3, ARF, Aux/IAA | AtARF18 |
OfARF19 | Contig389.17 | 14 | 685 | 76.95 | 6.06 | 52.79 | −0.436 | B3, ARF, Aux/IAA | AtARF18 |
OfARF20a | Contig267.9 | 14 | 680 | 76.3 | 6.26 | 55.17 | −0.516 | B3, ARF, Aux/IAA | AtARF18 |
OfARF20b | Contig390.3 | 14 | 686 | 77 | 6.19 | 55.97 | −0.514 | B3, ARF, Aux/IAA | AtARF18 |
OfARF21a | Contig314.6 | 14 | 893 | 98.79 | 6.11 | 67.35 | −0.362 | B3, ARF, Aux/IAA | AtARF6 |
OfARF21b | Contig236.41 | 14 | 893 | 98.5 | 5.74 | 65.08 | −0.339 | B3, ARF, Aux/IAA | AtARF6 |
OfARF22a | Contig109.86 | 14 | 890 | 98.99 | 6.2 | 67.24 | −0.454 | B3, ARF, Aux/IAA | AtARF6 |
OfARF22b | Contig154.52 | 14 | 898 | 99.9 | 6.07 | 68.19 | −0.462 | B3, ARF, Aux/IAA | AtARF6 |
OfARF23 | Contig72.89 | 15 | 763 | 86.2 | 6.16 | 61.71 | −0.456 | B3, ARF, Aux/IAA | AtARF8 |
OfARF24a | Contig189.73 | 14 | 838 | 93.16 | 6.04 | 57.06 | −0.445 | B3, ARF, Aux/IAA | AtARF8 |
OfARF24b | Contig165.100 | 14 | 839 | 93.65 | 6.04 | 57.64 | −0.478 | B3, ARF, Aux/IAA | AtARF8 |
OfARF25a | Contig158.77 | 14 | 935 | 103.58 | 5.35 | 56.60 | −0.440 | B3, ARF, Aux/IAA | AtARF5 |
OfARF25b | Contig16.261 | 15 | 809 | 90.34 | 5.22 | 56.51 | −0.292 | ARF, Aux/IAA | AtARF5 |
OfARF26a | Contig183.139 | 13 | 1026 | 113.47 | 6.16 | 61.78 | −0.567 | B3, ARF, Aux/IAA | AtARF7 |
OfARF26b | Contig259.21 | 13 | 1028 | 113.72 | 6.16 | 62.17 | −0.573 | B3, ARF, Aux/IAA | AtARF7 |
OfARF27 | Contig248.99 | 11 | 390 | 43.46 | 8.26 | 64.10 | −0.282 | B3, ARF | AtARF7 |
OfARF28a | Contig312.37 | 14 | 1091 | 120.3 | 6.07 | 56.21 | −0.516 | B3, ARF, Aux/IAA | AtARF7 |
OfARF28b | Contig116.35 | 14 | 1078 | 119.52 | 6.17 | 56.52 | −0.512 | B3, ARF, Aux/IAA | AtARF7 |
OfARF29a | Contig132.116 | 15 | 964 | 106.71 | 6.44 | 58.78 | −0.555 | B3, ARF, Aux/IAA | AtARF7 |
OfARF29b | Contig8.81 | 14 | 1108 | 122.67 | 6.3 | 57.79 | −0.553 | B3, ARF, Aux/IAA | AtARF7 |
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Chen, G.; Yue, Y.; Li, L.; Li, Y.; Li, H.; Ding, W.; Shi, T.; Yang, X.; Wang, L. Genome-Wide Identification of the Auxin Response Factor (ARF) Gene Family and Their Expression Analysis during Flower Development of Osmanthus fragrans. Forests 2020, 11, 245. https://doi.org/10.3390/f11020245
Chen G, Yue Y, Li L, Li Y, Li H, Ding W, Shi T, Yang X, Wang L. Genome-Wide Identification of the Auxin Response Factor (ARF) Gene Family and Their Expression Analysis during Flower Development of Osmanthus fragrans. Forests. 2020; 11(2):245. https://doi.org/10.3390/f11020245
Chicago/Turabian StyleChen, Gongwei, Yuanzheng Yue, Ling Li, Yuli Li, Haiyan Li, Wenjie Ding, Tingting Shi, Xiulian Yang, and Lianggui Wang. 2020. "Genome-Wide Identification of the Auxin Response Factor (ARF) Gene Family and Their Expression Analysis during Flower Development of Osmanthus fragrans" Forests 11, no. 2: 245. https://doi.org/10.3390/f11020245
APA StyleChen, G., Yue, Y., Li, L., Li, Y., Li, H., Ding, W., Shi, T., Yang, X., & Wang, L. (2020). Genome-Wide Identification of the Auxin Response Factor (ARF) Gene Family and Their Expression Analysis during Flower Development of Osmanthus fragrans. Forests, 11(2), 245. https://doi.org/10.3390/f11020245