Investigation of the EIL/EIN3 Transcription Factor Gene Family Members and Their Expression Levels in the Early Stage of Cotton Fiber Development
Abstract
:1. Introduction
2. Materials and Methods
2.1. Gene Identification Procedures
2.2. Phylogenetic Analysis of the EIL/EIN3 Protein Family
2.3. Analysis of Cis-Acting Regulatory Elements and miRNA Targets
2.4. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Analysis of EIL/EIN3 Genes
2.5. Protein Interaction Networks of EIL/EIN3 Genes
2.6. Plant Material, RNA-seq, and Data Analysis
3. Results and Discussion
3.1. Gene Identification Procedures
3.2. Gene Structure Analysis and Conserved Motif Analysis of EIL/EIN3 Genes
3.3. Phylogeny of EIL/EIN3 Members
3.4. Cis-Regulatory Element Analysis
3.5. GO and KEGG Pathway Analysis of EIL/EIN3 Genes
3.6. Protein–Protein Interaction Networks of EIL/EIN3 Genes
3.7. Expression Level Analysis of Cotton EIL/EIN3 Genes
3.8. Prediction of miRNA Targets in Cotton EIL/EIN3 Genes during Cotton Fiber Development
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Availability of Materials and Data
References
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Gene ID | Protein Domain | Chro No. | Start | End | Protein Length | Isoelectric Point | Molecular Weight | Localization |
---|---|---|---|---|---|---|---|---|
Gh_A02G1256 | EIN3 | Ah02 | 74,321,882 | 74,323,399 | 505 | 5.06 | 57,338.59 | Nucleus |
Gh_A03G2063 | EIL3 | Ah03 | 76,519 | 78,363 | 603 | 5.47 | 68,277.79 | Nucleus |
Gh_A05G0554 | EIL3 | Ah05 | 5,944,064 | 5,945,875 | 603 | 5.87 | 68,073.64 | Nucleus |
Gh_A05G0871 | EIN3 | Ah05 | 8,658,831 | 8,660,669 | 612 | 5.38 | 69,300.14 | Nucleus |
Gh_A06G0989 | EIL3 | Ah06 | 47,012,156 | 47,014,682 | 690 | 5.89 | 77,907.98 | Nucleus |
Gh_A08G1750 | EIN3 | Ah08 | 97,487,518 | 97,489,359 | 613 | 5.53 | 69,551.64 | Nucleus |
Gh_A13G1864 | EIL3 | Ah13 | 78,270,382 | 78,271,984 | 363 | 9.12 | 41,004.58 | Nucleus |
Gh_A13G2005 | EIN3 | Ah13 | 79,505,190 | 79,506,980 | 596 | 5.2 | 67,093.59 | Nucleus |
Gh_D03G0396 | EIL3 | Dh03 | 5,580,925 | 5,582,439 | 504 | 4.98 | 57,282.61 | Nucleus |
Gh_D03G1810 | EIN3 | Dh03 | 45,097 | 46,944 | 615 | 5.6 | 69,643.55 | Nucleus |
Gh_D05G3883 | EIN3 | Dh05 | 159,742 | 161,580 | 612 | 5.51 | 69,328.29 | Nucleus |
Gh_D06G1178 | EIL3 | Dh06 | 29,244,232 | 29,246,749 | 686 | 5.97 | 77,587.57 | Nucleus |
Gh_D07G1670 | EIN3 | Dh07 | 34,686,430 | 34,686,759 | 109 | 6.61 | 13,052.13 | Nucleus |
Gh_D08G2099 | EIN3 | Dh08 | 59,885,901 | 59,887,745 | 614 | 5.58 | 69,713.77 | Nucleus |
Gh_D12G2800 | EIN3 | Dh12 | 93,192 | 93,557 | 121 | 4.78 | 14,486.68 | Nucleus |
Gh_D13G2252 | EIL3 | Dh13 | 58,573,978 | 58,575,579 | 363 | 9.11 | 40,835.48 | Nucleus |
Gh_D13G2404 | EIN3 | Dh13 | 60,092,959 | 60,094,743 | 594 | 5.16 | 66,776.31 | Nucleus |
Gh_Sca006457G01 | EIL3 | scaffold6457 | 4225 | 8701 | 601 | 5.58 | 67,828.14 | Nucleus |
Gorai.001G192700 | EIN3 | Chr501 | 32,645,047 | 32,645,559 | 120 | 5.03 | 15,060.47 | Nucleus |
Gorai.003G043500 | EIL3 | Chr503 | 5,592,648 | 5,594,162 | 504 | 5.02 | 57,401.84 | Nucleus |
Gorai.003G140600 | EIN3 | Chr503 | 40,374,524 | 40,377,941 | 615 | 5.54 | 70,282.28 | Nucleus |
Gorai.004G227800 | EIN3 | Chr504 | 56,214,497 | 56,218,239 | 614 | 5.66 | 70,437.6 | Nucleus |
Gorai.007G241000 | EIL3 | Chr507 | 34,165,596 | 34,167,386 | 482 | 5.33 | 56,260.32 | Nucleus |
Gorai.009G071400 | EIL3 | Chr509 | 5,075,017 | 5,078,672 | 601 | 5.74 | 68,489.99 | Nucleus |
Gorai.009G105400 | EIN3 | Chr509 | 7,642,067 | 7,645,836 | 612 | 5.56 | 70,090.19 | Nucleus |
Gorai.010G128700 | EIL3 | Chr510 | 27,860,507 | 27,863,910 | 686 | 6.02 | 78,137.1 | Nucleus |
Gorai.013G250300 | EIL3 | Chr513 | 56,813,952 | 56,816,039 | 363 | 9.35 | 41,574.39 | Nucleus |
Gorai.013G266300 | EIN3 | Chr513 | 57,906,440 | 57,909,956 | 594 | 5.17 | 67,508.2 | Nucleus |
Ga01G2390 | EIN3 | Chr201 | 106,813,982 | 106,815,826 | 614 | 5.58 | 69,535.33 | Nucleus |
Ga02G0423 | EIL3 | Chr202 | 6,411,513 | 6,413,030 | 505 | 5.06 | 57,317.58 | Nucleus |
Ga05G0722 | EIL3 | Chr205 | 6,269,696 | 6,272,122 | 601 | 5.66 | 67,740.02 | Nucleus |
Ga05G1071 | EIN3 | Chr205 | 9,262,923 | 9,264,764 | 613 | 5.44 | 69,477.4 | Nucleus |
Ga06G1279 | EIL3 | Chr206 | 53,063,302 | 53,065,786 | 631 | 5.83 | 71,738.04 | Nucleus |
Ga08G2308 | EIN3 | Chr208 | 122,216,099 | 122,217,940 | 613 | 5.47 | 69,513.56 | Nucleus |
Ga13G2636 | EIL3 | Chr213 | 122,248,180 | 122,249,780 | 363 | 8.61 | 40,688.25 | Nucleus |
Ga13G2790 | EIN3 | Chr213 | 123,477,839 | 123,479,629 | 596 | 5.2 | 67,105.58 | Nucleus |
Ga14G2078 | EIL3 | tig00017874 | 3742 | 6220 | 663 | 5.88 | 75,328.17 | Nucleus |
miRNAs | Li1-0DPA | WT-0DPA | log2.Fold | q value | Li1-8DPA | WT-8DPA | log2.Fold | q value |
---|---|---|---|---|---|---|---|---|
ghr-miR156a | 296.01 | 153.324 | 0.94906 | 5.26 × 10−18 | 254.3824 | 350.725 | −0.4633 | 0.00071 |
ghr-miR156c | 49.3349 | 51.108 | −0.0509 | 0.057793 | 13.38854 | 58.4542 | −2.1263 | 3.65 × 10−8 |
ghr-miR169a | 0.77709 | 0.2271 | −0.1263 | 0.089546 | 26.77709 | 29.2271 | −0.1263 | 0.08955 |
ghr-miR394b | 17267.2 | 22589.7 | −0.3876 | 1.09 × 10−27 | 13910.7 | 18150 | −0.3838 | 1.49 × 10−52 |
ghr-miR7491 | 296.01 | 1226.59 | −2.0509 | 9.25 × 10−107 | 200.8282 | 233.817 | −0.2194 | 0.05341 |
ghr-miR7495a | 641.354 | 153.324 | 2.0645 | 3.97 × 10−89 | 240.9938 | 555.315 | −1.2043 | 4.48 × 10−24 |
ghr-miR7497 | 49.3349 | 51.108 | −0.0509 | 0.057793 | 13.38854 | 0 | 4.7429 | 1.49 × 10−5 |
ghr-miR7502 | 172.672 | 204.432 | −0.2436 | 0.099541 | 66.94272 | 146.135 | −1.1263 | 2.12 × 10−7 |
ghr-miR7504b | 493.349 | 766.62 | −0.6359 | 1.28 × 10−7 | 388.2678 | 409.179 | −0.0757 | 0.05005 |
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Salih, H.; He, S.; Li, H.; Peng, Z.; Du, X. Investigation of the EIL/EIN3 Transcription Factor Gene Family Members and Their Expression Levels in the Early Stage of Cotton Fiber Development. Plants 2020, 9, 128. https://doi.org/10.3390/plants9010128
Salih H, He S, Li H, Peng Z, Du X. Investigation of the EIL/EIN3 Transcription Factor Gene Family Members and Their Expression Levels in the Early Stage of Cotton Fiber Development. Plants. 2020; 9(1):128. https://doi.org/10.3390/plants9010128
Chicago/Turabian StyleSalih, Haron, Shoupu He, Hongge Li, Zhen Peng, and Xiongming Du. 2020. "Investigation of the EIL/EIN3 Transcription Factor Gene Family Members and Their Expression Levels in the Early Stage of Cotton Fiber Development" Plants 9, no. 1: 128. https://doi.org/10.3390/plants9010128