Genome-Wide Identification and Expression Analysis of the Cucumber FKBP Gene Family in Response to Abiotic and Biotic Stresses
Abstract
:1. Introduction
2. Materials and Methods
2.1. Identification and Chromosomal Distribution of Cucumber FKBP Genes
2.2. Phylogenetic Analysis of FKBP Family Genes from Cucumber, Arabidopsis, and Rice
2.3. Gene Structure, Conserved Motif, and Cis-Acting Elements Analyses of Cucumber FKBP Genes
2.4. Synteny Analysis of FKBP Family Genes from Cucumber, A. thaliana, and Rice
2.5. Tissue-Specific Expression Analysis of the Cucumber FKBP Family Genes
2.6. Expression Patterns Analysis of the Cucumber FKBP Family Genes under Various Stresses
2.7. Protein Interaction Analysis of FKBP Family Gene in Cucumber
3. Results
3.1. Identification and Physicochemical Characteristics of Cucumber FKBP Genes
3.2. Chromosome Distribution of Cucumber FKBP Genes
3.3. Phylogenetic Analysis of FKBP Family Genes in Cucumber, Arabidopsis, and Rice
3.4. Gene Structure and Conserved Motif Analysis of Cucumber FKBP Genes
3.5. Synteny Analysis of FKBP Genes among Cucumber, Arabidopsis, and Rice
3.6. Analysis of the Cis-Acting Elements in Cucumber FKBP Genes
3.7. Tissue-Specific Expression Analysis of Cucumber FKBP Genes
3.8. Expression Patterns Analysis of Cucumber FKBP Genes under Abiotic Stresses
3.9. Expression Patterns Analysis of Cucumber FKBP Genes under Biotic Stresses
3.10. Regulation Patterns of Cucumber FKBP Genes under Stresses
3.11. Protein–Protein Interaction Analysis of Cucumber FKBP Proteins and the CsaV3_1G007080 Protein
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Gene ID | CDS Size (bp) | Number of Amino Acid (aa) | Molecular Weight (kDa) | Theoretical pI | Instability Index | Aliphatic Index | Grand Average of Hydropathicity | Prediction of Subcellular Location |
---|---|---|---|---|---|---|---|---|
CsaV3_1G007080 | 759 | 252 | 26.96 | 6.76 | 48.72 | 81.98 | −0.25 | Chloroplast |
CsaV3_1G046550 | 678 | 225 | 24.48 | 7.89 | 53.13 | 81.56 | −0.11 | Chloroplast |
CsaV3_3G007570 | 783 | 260 | 29.38 | 9.17 | 60.58 | 68.19 | −0.517 | Chloroplast |
CsaV3_3G015840 | 1728 | 575 | 64.27 | 5.23 | 35.08 | 76.63 | −0.69 | Peroxisome |
CsaV3_3G016330 | 1524 | 507 | 56.14 | 5.55 | 43.65 | 61.28 | −1.044 | Nucleus |
CsaV3_3G032060 | 1110 | 369 | 42.17 | 5.61 | 36.60 | 73.25 | −0.66 | Cytoskeleton |
CsaV3_3G036610 | 696 | 231 | 24.71 | 9.41 | 52.50 | 89.44 | −0.142 | Chloroplast |
CsaV3_4G002230 | 774 | 257 | 27.95 | 8.90 | 35.49 | 76.61 | −0.248 | Chloroplast |
CsaV3_4G002650 | 684 | 227 | 24.34 | 5.97 | 50.79 | 91.06 | −0.116 | Chloroplast |
CsaV3_4G025730 | 1866 | 621 | 69.96 | 5.32 | 43.73 | 71.26 | −0.567 | Nucleus |
CsaV3_4G037510 | 684 | 227 | 24.75 | 9.49 | 60.44 | 78.59 | −0.483 | Nucleus |
CsaV3_6G001250 | 564 | 187 | 20.04 | 6.77 | 31.63 | 78.34 | −0.506 | Nucleus |
CsaV3_6G006170 | 1692 | 563 | 62.13 | 5.42 | 48.46 | 61.28 | −0.956 | Nucleus |
CsaV3_6G045680 | 648 | 215 | 22.57 | 8.63 | 43.99 | 85.26 | 0.021 | Chloroplast |
CsaV3_6G053090 | 645 | 214 | 22.40 | 9.23 | 31.06 | 88.88 | −0.01 | Chloroplast |
CsaV3_7G006970 | 339 | 112 | 11.94 | 7.76 | 30.67 | 73.93 | −0.171 | Chloroplast |
CsaV3_7G023830 | 576 | 191 | 21.73 | 5.76 | 43.00 | 93.77 | −0.192 | Cytoplasm |
CsaV3_7G026570 | 1626 | 541 | 60.17 | 5.45 | 25.01 | 81.48 | −0.554 | Cytoplasm |
CsaV3_7G026580 | 501 | 166 | 17.86 | 6.30 | 36.12 | 78.67 | −0.375 | Cytoplasm |
Motif | Sequence | Number of Amino Acids | Pfam Annotation |
---|---|---|---|
motif 1 | GVKGMKVGEKRRLTIPPELGYG | 22 | FKBP |
motif 2 | DDGRPFKFRLGEGQVIKGWDE | 21 | FKBP |
motif 3 | PNIPPNATLVFDVELVSV | 18 | FKBP |
motif 4 | PKDGDEVKVHYTGKLEDGTVF | 21 | FKBP |
motif 5 | QAKALKNPCNLNNAACKLKLKEYKEAEKLCTKV LELDSSNVKALYRRGQAYIQLGDLDLAEEDIKKA | 67 | - |
motif 6 | IPPSEYTTTPSGLKYYDIKVGSGP | 24 | - |
motif 7 | IEAAGKKKEEGNVLFKEGKFERASKRYEKAVRYIEYDSSF | 40 | - |
motif 8 | MGFWGIEVKPGKPFTQKFDDFKGKLRISQATLGFGSAKEKSILQCN | 46 | - |
motif 9 | VGNKSPIFLCSLFPEKIECCPLDLEFEEDEEIIFSVIGPRSIHLSGYFLGNCRH | 54 | - |
motif 10 | GVLKKILKEGEGWE | 14 | - |
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Yang, D.; Li, Y.; Zhu, M.; Cui, R.; Gao, J.; Shu, Y.; Lu, X.; Zhang, H.; Zhang, K. Genome-Wide Identification and Expression Analysis of the Cucumber FKBP Gene Family in Response to Abiotic and Biotic Stresses. Genes 2023, 14, 2006. https://doi.org/10.3390/genes14112006
Yang D, Li Y, Zhu M, Cui R, Gao J, Shu Y, Lu X, Zhang H, Zhang K. Genome-Wide Identification and Expression Analysis of the Cucumber FKBP Gene Family in Response to Abiotic and Biotic Stresses. Genes. 2023; 14(11):2006. https://doi.org/10.3390/genes14112006
Chicago/Turabian StyleYang, Dekun, Yahui Li, Mengdi Zhu, Rongjing Cui, Jiong Gao, Yingjie Shu, Xiaomin Lu, Huijun Zhang, and Kaijing Zhang. 2023. "Genome-Wide Identification and Expression Analysis of the Cucumber FKBP Gene Family in Response to Abiotic and Biotic Stresses" Genes 14, no. 11: 2006. https://doi.org/10.3390/genes14112006
APA StyleYang, D., Li, Y., Zhu, M., Cui, R., Gao, J., Shu, Y., Lu, X., Zhang, H., & Zhang, K. (2023). Genome-Wide Identification and Expression Analysis of the Cucumber FKBP Gene Family in Response to Abiotic and Biotic Stresses. Genes, 14(11), 2006. https://doi.org/10.3390/genes14112006