Genome-Wide Analysis of Q-Type C2H2 ZFP Genes in Response to Biotic and Abiotic Stresses in Sugar Beet
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Acquisition of the Sequences of the Q-Type ZFP Transcription Factor Family in Sugar Beet
2.2. Chromosomal Distribution, Protein Characterization, and Amino Acid Properties
2.3. Multiple Sequence Alignment and Phylogenetic Tree Construction
2.4. Analysis of Members of the C2H2 ZFP Gene Family
2.5. Promoter Analysis of the BvZFP Genes in Sugar Beet
2.6. Collinearity Analysis of Arabidopsis and Sugar Beet BvZFP Genes
2.7. BvZFP Genes Expression Network Analysis
3. Results
3.1. Identification and Chromosomal Localization of the C2H2 Q-Type ZFP Subclass in Sugar Beet
3.2. Characterization of the Sugar Beet C2H2 Q-Type ZFP Subclass
3.3. Phylogenetic Analysis of Q-Type BvZFP Genes
3.4. Gene Structure and Conservative Motif Analysis of C2H2 Q-Type BvZFPs
3.5. Genomic Collinearity Analysis of C2H2 Q-Type BvZFPs between Sugar Beet and Arabidopsis
3.6. Promoter Analysis of the Q-Type BVZFP Genes in Sugar Beet
3.7. Expression Profiles Analysis of Q-Type BvZFPs in Different Tissue
3.8. Responses of Q-Type BvZFP Genes under Salt Treatment and Viral Infection
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene Name | Gene ID | Amino Acid/aa | ORF/bp | Molecular Weight | pI | Instability Index | GRAVY | Location | Subcellular Localization | Group | |
---|---|---|---|---|---|---|---|---|---|---|---|
BvZFP1 | LOC104905560 | 541 | 1623 | 58,633.75 | 6.86 | 57.91 | −0.786 | 10,695,460 | 10,697,687 | Nucleus | 3i |
BvZFP2 | LOC125495709 | 367 | 1101 | 41,279.25 | 8.02 | 55.83 | −0.862 | 10,706,247 | 10,708,429 | Nucleus | 3i |
BvZFP3 | LOC104898669 | 456 | 1368 | 50,063.48 | 6.01 | 60.88 | −1.002 | 36,219,959 | 36,222,487 | Nucleus | 2i |
BvZFP4 | LOC104887623 | 283 | 849 | 31,507.39 | 8.21 | 41.25 | −0.667 | 4,757,460 | 4,758,311 | Nucleus | 1i |
BvZFP5 | LOC104906182 | 543 | 1629 | 60,544.44 | 7.17 | 59.45 | −0.701 | 14,363,882 | 14,366,296 | Nucleus | 3i |
BvZFP6 | LOC104886969 | 186 | 558 | 20,667.45 | 8.86 | 57.6 | −0.506 | 29,939,770 | 29,940,614 | Nucleus | 2i |
BvZFP7 | LOC104883124 | 278 | 834 | 30,386.53 | 6.13 | 59.97 | −0.644 | 45,479,878 | 45,480,934 | Nucleus | 1i |
BvZFP8 | LOC104883624 | 179 | 537 | 20,615.07 | 8.3 | 54.73 | −0.976 | 52,215,194 | 52,216,003 | Nucleus | 1i |
BvZFP9 | LOC104906611 | 170 | 510 | 18,959.88 | 6.65 | 65.03 | −0.922 | 11,875,979 | 11,876,976 | Nucleus | 1i |
BvZFP10 | LOC104906657 | 255 | 765 | 28,493.69 | 9.22 | 57.02 | −0.867 | 11,959,217 | 11,959,984 | Nucleus | 1i |
BvZFP11 | LOC104888927 | 232 | 696 | 26,701.97 | 6.89 | 67.24 | −0.791 | 12,886,752 | 12,888,260 | Nucleus | 1i |
BvZFP12 | LOC104906753 | 304 | 912 | 33,684.31 | 8.85 | 43.09 | −1.037 | 43,115,842 | 43,118,169 | Nucleus | 1i |
BvZFP13 | LOC104889553 | 323 | 969 | 35,834.41 | 8.56 | 58.9 | −0.805 | 51,214,957 | 51,215,928 | Nucleus | 1i |
BvZFP14 | LOC104907233 | 277 | 831 | 31,391.42 | 6.2 | 58.48 | −0.972 | 8,025,899 | 8,027,395 | Nucleus | 1i |
BvZFP15 | LOC104890281 | 572 | 1716 | 62,896.02 | 5.69 | 58.76 | −1.132 | 57,253,629 | 57,255,347 | Nucleus | 3i |
BvZFP16 | LOC104894695 | 162 | 486 | 18,233.83 | 6.1 | 58.33 | −1.089 | 405,412 | 405,900 | Nucleus | 1i |
BvZFP17 | LOC104893969 | 496 | 1488 | 54,927.45 | 8.48 | 66.19 | −0.718 | 10,823,448 | 10,825,115 | Nucleus | 3i |
BvZFP18 | LOC104892924 | 177 | 531 | 20,328.6 | 5.97 | 61.13 | −0.759 | 43,735,292 | 43,736,429 | Nucleus | 1i |
BvZFP19 | LOC104897252 | 226 | 678 | 25,693.54 | 9.1 | 57.43 | −0.892 | 10,200,725 | 10,201,830 | Nucleus | 1i |
BvZFP20 | LOC104896450 | 247 | 741 | 25,939.68 | 8.64 | 46.76 | −0.604 | 34,971,928 | 34,972,995 | Nucleus | 1i |
BvZFP21 | LOC104896549 | 220 | 660 | 24,314.02 | 7.24 | 54.26 | −0.921 | 36,683,224 | 36,687,039 | Nucleus | 1i |
BvZFP22 | LOC104895813 | 613 | 1839 | 68,769.06 | 6.91 | 48.17 | −1.27 | 53,568,797 | 53,571,334 | Nucleus | 4i |
BvZFP23 | LOC104895001 | 179 | 537 | 19,911.57 | 8.99 | 75.14 | −0.496 | 63,541,505 | 63,542,044 | Nucleus | 1i |
BvZFP24 | LOC104885426 | 177 | 531 | 19,942.29 | 6.15 | 49.73 | −0.751 | 64,317,253 | 64,317,786 | Nucleus | 1i |
BvZFP25 | LOC104885142 | 165 | 495 | 18,957.43 | 7.75 | 37.2 | −0.788 | 64,323,220 | 64,323,717 | Nucleus | 1i |
BvZFP26 | LOC104884472 | 181 | 543 | 20,434.76 | 8.32 | 43.2 | −0.842 | 64,406,993 | 64,407,538 | Nucleus | 1i |
BvZFP27 | LOC104900166 | 245 | 735 | 26,613.84 | 6.01 | 65.67 | −0.521 | 2,250,266 | 2,251,688 | Nucleus | 2i |
BvZFP28 | LOC104908846 | 340 | 1020 | 37,135.81 | 7.75 | 62.32 | −0.839 | 13,404,684 | 13,406,826 | Nucleus | 2i |
BvZFP29 | LOC104899451 | 204 | 612 | 22,977.76 | 8.79 | 47.89 | −0.777 | 47,440,915 | 47,443,048 | Nucleus | 1i |
BvZFP30 | LOC104901462 | 242 | 726 | 25,661.67 | 8.09 | 62.93 | −0.545 | 21,006,400 | 21,007,514 | Nucleus | 2i |
BvZFP31 | LOC104904162 | 237 | 711 | 25,331.76 | 8.55 | 54.27 | −0.358 | 19,929,210 | 19,930,057 | Nucleus | 3i |
BvZFP32 | LOC104904895 | 299 | 897 | 33,574.34 | 8.24 | 50.67 | −0.682 | 33,331,932 | 33,333,327 | Nucleus | 1i |
BvZFP33 | LOC104904924 | 185 | 555 | 21,039.05 | 8.76 | 59.64 | −0.511 | 33,657,441 | 33,658,524 | Nucleus | 1i |
BvZFP34 | LOC104902980 | 342 | 1026 | 37,289.83 | 6.21 | 58.69 | −0.823 | 44,803,778 | 44,805,047 | Nucleus | 2i |
BvZFP35 | LOC104893645 | 237 | 711 | 26,905.18 | 8.52 | 67.93 | −0.792 | 1,955,234 | 1,956,376 | Nucleus | 1i |
Species | The Number of C2H2 ZFPs | The Number of Q-Type | The Number of EAR Motif | Reference |
---|---|---|---|---|
G. max | 321 | 130 | -- | [8] |
B. rapa | 301 | 110 | -- | [9] |
M. sativa | -- | 58 | -- | [34] |
M. truncatula | 218 | 71 | 106 | [10] |
Z. mays | 326 | 147 | -- | [52] |
T. aestivum | 204 | 159 | 68 | [11] |
O. sativa | 189 | 72 | 43 | [12] |
A. thaliana | 176 | 64 | -- | [20] |
S. bicolor | 145 | -- | -- | [15] |
C. sativus | 129 | 52 | -- | [16] |
Dactylis glomerata | 125 | 50 | -- | [53] |
Setaria italica | 124 | 97 | -- | [54] |
Triticum turgidum | 122 | 96 | 11 | [55] |
Nicotiana tabacum | 118 | 118 | -- | [56] |
P. trichocarpa | 109 | 62 | 16 | [17] |
S. lycopersicum | 104 | 54 | -- | [18] |
V. vinifera | 98 | 65 | 49 | [57] |
Capsicum annuum | 79 | 37 | 41 | [51] |
S. tuberosum | -- | 79 | 54 | [58] |
B. oleracea | -- | 37 | -- | [33] |
B. vulgaris | 104 | 35 | 32 |
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Li, M.; Dong, X.; Long, G.; Zhang, Z.; Han, C.; Wang, Y. Genome-Wide Analysis of Q-Type C2H2 ZFP Genes in Response to Biotic and Abiotic Stresses in Sugar Beet. Biology 2023, 12, 1309. https://doi.org/10.3390/biology12101309
Li M, Dong X, Long G, Zhang Z, Han C, Wang Y. Genome-Wide Analysis of Q-Type C2H2 ZFP Genes in Response to Biotic and Abiotic Stresses in Sugar Beet. Biology. 2023; 12(10):1309. https://doi.org/10.3390/biology12101309
Chicago/Turabian StyleLi, Menglin, Xuanyu Dong, Guozhang Long, Zongying Zhang, Chenggui Han, and Ying Wang. 2023. "Genome-Wide Analysis of Q-Type C2H2 ZFP Genes in Response to Biotic and Abiotic Stresses in Sugar Beet" Biology 12, no. 10: 1309. https://doi.org/10.3390/biology12101309
APA StyleLi, M., Dong, X., Long, G., Zhang, Z., Han, C., & Wang, Y. (2023). Genome-Wide Analysis of Q-Type C2H2 ZFP Genes in Response to Biotic and Abiotic Stresses in Sugar Beet. Biology, 12(10), 1309. https://doi.org/10.3390/biology12101309