In Silico Analysis of the MAPK Gene Family in Cabbage and Its Expression during Development and Stress Response
<p>Protein sequence comparison of cabbage MAPK proteins using DNAMAN software. The T(E/D)Y, IGxGxYGxV and (LH)DXXDE(P)XC domains are marked by red boxes.</p> "> Figure 2
<p>Phylogenetic tree of MAPK gene family in <span class="html-italic">B. oleracea</span> (<span class="html-italic">Bo</span>), <span class="html-italic">B. rapa</span> (<span class="html-italic">Bra</span>), <span class="html-italic">B. napus</span> (<span class="html-italic">Bna</span>), <span class="html-italic">A. thaliana</span> (<span class="html-italic">At</span>), and <span class="html-italic">O.sativa</span> (<span class="html-italic">Os</span>). The tree was constructed based on the full length of MAPK protein sequences with MEGA5.0 and the neighbor-joining method. MAPK proteins were divided into four subgroups (A, B, C, and D). The red circle represents <span class="html-italic">B. oleracea</span> MAPK (BoMAPK); pink square represents <span class="html-italic">B. rapa</span> MAPK; green diamond represents <span class="html-italic">B. napus</span> MAPK (BnaMAPK); blue triangle represents <span class="html-italic">A. thaliana</span> MAPK (AtMAPK); and the green hollow circle represents <span class="html-italic">O. sativa</span> MAPK (OsMAPK).</p> "> Figure 3
<p>Chromosomal distributions of <span class="html-italic">BoMAPK</span> genes. The vertical bars mark the chromosomes of cabbage. Chromosome numbers are on the left of each chromosome. The left most scale indicates the length of the chromosome.</p> "> Figure 4
<p>Structural analysis of cabbage MAPK gene family. The phylogenetic tree of cabbage MAPK proteins on the left; the motif composition in the middle; the exon-intron structure of cabbage <span class="html-italic">MAPK</span> genes on the right.</p> "> Figure 5
<p><span class="html-italic">Cis</span>-element analysis of <span class="html-italic">BoMAPKs</span> promoter. Analysis of <span class="html-italic">cis</span>-regulatory elements in promoter regions of 24 <span class="html-italic">BoMAPKs</span>. The black line indicates the promoter length of each <span class="html-italic">BoMAPK</span> gene. The boxes with different colors represent different types of <span class="html-italic">cis</span>-acting elements.</p> "> Figure 6
<p>An interaction network analysis of BoMAPK proteins according to STRING. The nodes represent proteins, the lines between nodes indicate the interaction between proteins, and different colors correspond to different interaction types.</p> "> Figure 7
<p>Heatmap showing the expression profile of <span class="html-italic">BoMAPK</span> genes in different tissues.</p> "> Figure 8
<p>Expression analysis of <span class="html-italic">BoMAPK</span> genes under culbroot infection using RT-qPCR. F7I: roots of cabbage seedlings at 7 days after inoculation, F7CK: untreated roots of cabbage seedlings after 7 days, F21I: roots of cabbage seedlings at day 21 after inoculation, F21CK: untreated roots of cabbage seedlings at day 21. Lowercase letters represent significant differences (<span class="html-italic">p</span> < 0.05).</p> "> Figure 9
<p>Expression analysis of <span class="html-italic">BoMAPK</span> genes under two abiotic stresses using RT-qPCR. (<b>A</b>) The relative expression level of <span class="html-italic">BoMAPK</span> genes under Nacl stress. (<b>B</b>) The relative expression level of <span class="html-italic">BoMAPK</span> genes under cold stress.</p> ">
Abstract
:1. Introduction
2. Materials and Methods
2.1. Identification and In Silico Analysis of MAPK Family Members in Cabbage
2.2. Multiple Sequence Alignment and Construction of Phylogenetic Tree
2.3. Chromosomal Localization and Synteny Analysis of BoMAPK Genes
2.4. Gene Structure and Motif Analysis of BoMAPK Genes
2.5. Cis-Acting Elements Analysis in BoMAPK Genes Promoter
2.6. Expression Profiles of BoMAPK Genes in Different Tissues
2.7. Plant Materials and Treatment Methods
2.8. RNA Extraction and RT-qPCR
2.9. Protein–protein Interaction Network Prediction
3. Results
3.1. Identification of MAPK Gene Family Members in Cabbage
3.2. Phylogenetic Analysis of BoMAPK Gene Family
3.3. Chromosome Location and Synteny Analysis of BoMAPK Genes
3.4. Conserved Motifs and Gene Structure Analysis of BoMAPK Gene Family
3.5. Number and Types of Cis-Acting Elements of BoMAPK Genes Promoter
3.6. Prediction and Analysis of Protein–protein Interaction Network
3.7. Expression Analysis of BoMAPKs in Different Tissues and Development
3.8. Expression Pattern of BoMAPKs under Clubroot Disease Infection
3.9. Expression Profiles of BoMAPKs under Cold and Salt Stress Treatment
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Gene Name | Gene ID | Number of AA | MW (Da) | pI | AI | GRAVY | Localization Prediction |
---|---|---|---|---|---|---|---|
BoMAPK1 | BolC05g008000.2J | 369 | 42,485.25 | 6.67 | 98.27 | −0.248 | Cytoplasm |
BoMAPK2 | BolC01g035020.2J | 370 | 42,488.03 | 6.23 | 98.78 | −0.223 | Cytoplasm |
BoMAPK3 | BolC03g065400.2J | 370 | 42,592.77 | 5.70 | 92.00 | −0.312 | Cytoskeleton |
BoMAPK4.1 | BolC03g035260.2J | 373 | 42,513.48 | 5.85 | 89.14 | −0.332 | Cytoplasm |
BoMAPK4.2 | BolC08g057380.2J | 371 | 43,151.41 | 5.10 | 89.60 | −0.371 | Cytoplasm |
BoMAPK5 | BolC09g032170.2J | 373 | 42,809.88 | 5.57 | 91.98 | −0.302 | Cytoplasm |
BoMAPK6.1 | BolC04g005090.2J | 392 | 44,850.29 | 5.27 | 91.35 | −0.299 | Nucleus |
BoMAPK6.2 | BolC03g026650.2J | 414 | 47,076.99 | 5.35 | 93.12 | −0.220 | Chloroplast |
BoMAPK7 | BolC09g012900.2J | 368 | 42,234.85 | 7.18 | 94.29 | −0.238 | Cytoplasm |
BoMAPK8.1 | BolC08g051030.2J | 582 | 65,637.18 | 6.57 | 77.42 | −0.554 | Cytoplasm |
BoMAPK8.2 | BolC05g015790.2J | 584 | 65,863.30 | 6.08 | 78.51 | −0.527 | Chloroplast |
BoMAPK9 | BolC05g047830.2J | 501 | 57,381.46 | 8.12 | 80.06 | −0.479 | Cytoplasm |
BoMAPK13 | BolC04g067890.2J | 372 | 42,589.85 | 8.03 | 88.79 | −0.305 | Cytoplasm |
BoMAPK15 | BolC06g032120.2J | 577 | 65,327.03 | 7.29 | 80.12 | −0.571 | Cytoplasm |
BoMAPK16.1 | BolC09g053590.2J | 567 | 64,784.07 | 8.81 | 77.23 | −0.517 | Mitochondrion |
BoMAPK16.2 | BolC03g009910.2J | 698 | 79,579.79 | 9.27 | 76.98 | −0.549 | Chloroplast |
BoMAPK17.1 | BolC07g031210.2J | 487 | 55,627.59 | 6.51 | 81.25 | −0.419 | Cytoplasm |
BoMAPK17.2 | BolC02g049250.2J | 488 | 55,755.70 | 6.64 | 80.68 | −0.434 | Cytoplasm |
BoMAPK18.1 | BolC06g008540.2J | 602 | 67,838.36 | 9.20 | 76.64 | −0.446 | Nucleus |
BoMAPK18.2 | BolC05g051570.2J | 596 | 67,131.79 | 9.26 | 78.05 | −0.476 | Nucleus |
BoMAPK19.1 | BolC06g014820.2J | 561 | 63,486.84 | 9.27 | 83.28 | −0.377 | Chloroplast |
BoMAPK19.2 | BolC01g048030.2J | 648 | 72,685.31 | 9.48 | 78.12 | −0.465 | Chloroplast |
BoMAPK20.1 | BolC04g004430.2J | 840 | 95,445.32 | 9.00 | 76.42 | −0.460 | Nucleus |
BoMAPK20.2 | BolC03g026050.2J | 624 | 70,463.18 | 8.58 | 81.97 | −0.450 | Cytoplasm |
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Wang, M.; Chen, J.; Zhu, X.; Tai, X.; Bo, T. In Silico Analysis of the MAPK Gene Family in Cabbage and Its Expression during Development and Stress Response. Horticulturae 2023, 9, 1119. https://doi.org/10.3390/horticulturae9101119
Wang M, Chen J, Zhu X, Tai X, Bo T. In Silico Analysis of the MAPK Gene Family in Cabbage and Its Expression during Development and Stress Response. Horticulturae. 2023; 9(10):1119. https://doi.org/10.3390/horticulturae9101119
Chicago/Turabian StyleWang, Min, Jinxiu Chen, Xiaowei Zhu, Xiang Tai, and Tianyue Bo. 2023. "In Silico Analysis of the MAPK Gene Family in Cabbage and Its Expression during Development and Stress Response" Horticulturae 9, no. 10: 1119. https://doi.org/10.3390/horticulturae9101119
APA StyleWang, M., Chen, J., Zhu, X., Tai, X., & Bo, T. (2023). In Silico Analysis of the MAPK Gene Family in Cabbage and Its Expression during Development and Stress Response. Horticulturae, 9(10), 1119. https://doi.org/10.3390/horticulturae9101119