Identification and Expression Analysis of MPK and MKK Gene Families in Pecan (Carya illinoinensis)
Abstract
:1. Introduction
2. Results
2.1. Identification, Nomenclature, and Protein Sequence Analysis of MPK and MKK Gene Families
2.2. Phylogenetic Relationship of MPK and MKK Cascade Genes
2.3. Conserved Domains, Motifs, and Gene Structure Analysis in MPK and MKK Cascades
2.4. Analysis of Cis-Acting Elements in the Promoter Regions of MPK and MKK Genes
2.5. Genome Distribution and Gene Duplication of CiPawMPKs and CiPawMKKs
2.6. Expression Patterns and Co-Expression Networks of MPK and MKK in Different Organs of Pecan
2.7. Real-Time Quantitative Analysis of CiawMPK and CiPawMKK under Various Phytohormone Treatments and Abiotic or Biotic Stresses
2.8. Changes of SOD and POD Activity in Pecan Treated with NaCl and 20% PEG
3. Discussion
4. Materials and Methods
4.1. Genome-Wide Identification of MPK and MKK Gene Family in Pecan
4.2. Sequence Characterization Analysis
4.3. Multiple Sequence Alignment Analysis
4.4. Exon-Intron Structure and Conserved Motif Analysis
4.5. Construction and Analysis of Phylogenetic Tree
4.6. Cis-Acting Element Analysis
4.7. Gene Distribution Prediction
4.8. Gene Duplication Analysis and Ka/Ks Value Calculation
4.9. Plant Material, Growth Conditions, Treatments, and Sample Collection
4.10. RNA Extraction and qRT-PCR Analysis
4.11. Transcriptome and Co-expression Analysis of Pecan in Different Organs
4.12. Detection of Enzyme Activity
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Conflicts of Interest
References
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Gene Pairs | Ka | Ks | Ka/Ks |
---|---|---|---|
CiPawMPK4-2/CiPawMPK4-3 | 0.0495 | 1.2872 | 0.0385 |
CiPawMPK16-1/CiPawMPK16-2 | 0.0175 | 0.2601 | 0.0672 |
CiPaw.MKK2-1/CiPawMKK2-2 | 0.0332 | 0.2276 | 0.1457 |
CiPawMKK6-1/CiPawMKK6-2 | 0.0225 | 0.2606 | 0.0865 |
CiPawMKK5-1/CiPawMKK5-2 | 0.0753 | 0.3572 | 0.2108 |
CiPawMPK1/AtMPK2 | 0.0414 | 2.9663 | 0.0139 |
CiPawMPK4-3/AtMPK4 | 0.0179 | 1.7541 | 0.0102 |
CiPawMPK4-2/AtMPK5 | 0.0386 | 1.4692 | 0.0262 |
CiPawMPK6-1/AtMPK6 | 0.0152 | 1.9237 | 0.0079 |
CiPawMPK1/AtMPK7 | 0.0681 | — | — |
CiPawMPK9-2/AtMPK8 | 0.0303 | 1.4757 | 0.0205 |
CiPawMPK9-2/AtMPK9 | 0.0251 | 1.8535 | 0.0135 |
CiPawMPK6-1/AtMPK10 | 0.0971 | — | — |
CiPawMPK4-3/AtMPK11 | 0.0362 | 2.6224 | 0.0138 |
CiPawMPK4-3/AtMPK12 | 0.0689 | — | — |
CiPawMPK3-1/AtMPK13 | 0.1766 | — | — |
CiPawMPK1/AtMPK14 | 0.0933 | 2.4142 | 0.0387 |
CiPawMPK9-2/AtMPK15 | 0.0458 | 1.0731 | 0.0427 |
CiPawMPK16-2/AtMPK16 | 0.0150 | 0.9426 | 0.0159 |
CiPawMPK9-3/AtMPK17 | 0.0808 | — | — |
CiPawMPK19/AtMPK18 | 0.0248 | 1.4943 | 0.0166 |
CiPawMPK19/AtMPK19 | 0.0298 | 1.6066 | 0.0186 |
CiPawMKK2-1/AtMKK1 | 0.2114 | 1.9369 | 0.1091 |
CiPawMKK2-2/AtMKK2 | 0.1628 | 1.6321 | 0.0997 |
CiPawMKK3/AtMKK3 | 0.0673 | 1.5936 | 0.0422 |
CiPaw.MKK6-1/AtMKK6 | 0.0304 | 1.1024 | 0.0275 |
CiPawMKK9-2/AtMKK7 | 0.2316 | — | — |
CiPawMKK9-2/AtMKK9 | 0.2139 | — | — |
CiPawMKK10/AtMKK10 | 0.2998 | — | — |
CiPawMPK3-2/OsMPK3 | 0.0909 | — | — |
CiPawMKK5-2/OsMKK4 | 0.1923 | 0.8339 | 0.2306 |
CiPawMKK5-2/OsMKK5 | 0.1852 | 0.9013 | 0.2055 |
CiPawMKK10/OsMKK10-1 | 0.3306 | — | — |
CiPawMKK9-2/OsMKK10-3 | 0.3284 | 1.0807 | 0.3038 |
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Zhao, J.; Zhu, K.; Chen, M.; Ma, W.; Liu, J.; Tan, P.; Peng, F. Identification and Expression Analysis of MPK and MKK Gene Families in Pecan (Carya illinoinensis). Int. J. Mol. Sci. 2022, 23, 15190. https://doi.org/10.3390/ijms232315190
Zhao J, Zhu K, Chen M, Ma W, Liu J, Tan P, Peng F. Identification and Expression Analysis of MPK and MKK Gene Families in Pecan (Carya illinoinensis). International Journal of Molecular Sciences. 2022; 23(23):15190. https://doi.org/10.3390/ijms232315190
Chicago/Turabian StyleZhao, Juan, Kaikai Zhu, Mengyun Chen, Wenjuan Ma, Junping Liu, Pengpeng Tan, and Fangren Peng. 2022. "Identification and Expression Analysis of MPK and MKK Gene Families in Pecan (Carya illinoinensis)" International Journal of Molecular Sciences 23, no. 23: 15190. https://doi.org/10.3390/ijms232315190