Identification of the bZIP Gene Family and Investigation of Their Response to Drought Stress in Dendrobium catenatum
<p>Phylogenetic analyses of bZIP proteins from <span class="html-italic">D. catenatum</span>, <span class="html-italic">Arabidopsis</span> and rice. A phylogenetic tree of bZIP proteins was constructed using MEGA 6.0 software. The 10 subgroups are indicated by different colors and different colored letters. The blue circles represent <span class="html-italic">A. thaliana</span> bZIPs (AtbZIPs), the red stars represent <span class="html-italic">D. catenatum</span> bZIPs (DcbZIPs) and the black triangles represent <span class="html-italic">O. sativa</span> bZIPs (OsbZIPs).</p> "> Figure 2
<p>Motifs, structures and phylogenetic relationships of DcbZIP family members. (<b>A</b>) A phylogenetic tree of 62 DcbZIP proteins constructed using the maximum likelihood method. The different subgroups are indicated by different background colors and letters. (<b>B</b>) Conserved motifs of DcbZIP proteins. Different motifs are represented by different colored boxes. (<b>C</b>) Exon/intron structures of <span class="html-italic">DcbZIP</span> genes with UTR(s), exon(s) and intron(s) indicated with green boxes, yellow boxes and black lines, respectively. The phylogenetic tree, conserved motifs and gene structures were predicted with TBtools.</p> "> Figure 3
<p>Analysis of <span class="html-italic">cis</span>-elements in the <span class="html-italic">DcbZIP</span> genes promoter regions. (<b>A</b>) A phylogenetic tree of 62 DcbZIP proteins was constructed with the ML method. The different subgroups are indicated by different background colors and letters. (<b>B</b>) The different colored blocks represent the different types of <span class="html-italic">cis</span>-elements and their locations in each <span class="html-italic">DcbZIP</span> gene. (<b>C</b>) The different colors and numbers in the grid indicate the numbers of different promoter elements in the <span class="html-italic">DcbZIP</span> genes. The types, numbers and locations of potential elements in the promoter regions 2-kb upstream of the <span class="html-italic">DcbZIP</span> genes were analyzed by PlantCARE.</p> "> Figure 4
<p>Hierarchical clustering of <span class="html-italic">DcbZIP</span> genes expression profiles across different <span class="html-italic">D. catenatum</span> tissues. Data were normalized relative to each gene’s mean expression value across all tissues and log2−transformed. TPM (transcripts per million) values were used to create heat maps showing the expressions of <span class="html-italic">DcbZIP</span> genes in different tissues. The expression level ranges from low expression (green) to high expression (red).</p> "> Figure 5
<p>The expression patterns of <span class="html-italic">DcbZIP</span> genes evaluated by RNA-seq. The left heatmap shows the expressions of <span class="html-italic">DcbZIP</span> genes under different volumetric water contents of base material. Data were normalized relative to each gene’s mean expression value across all treatments and log2-transformed. TPM (transcripts per million) values were used to create heat map showing the expression of <span class="html-italic">DcbZIP</span> genes. The expression levels range from low expression (green) to high expression (red). The right heatmap shows the TPM ratios, with high ratios in light orange and low ratios in cyan. T1 was equal to the TPM of 10–15% divided by the TPM of 30–35%, and T2 was equal to the TPM of 0% divided by the TPM of 30–35%. Ranges of 30–35%, 10–15% and 0% represent the volumetric water content of the base material declining to ~30–35%, ~10–15% and ~0%, respectively.</p> "> Figure 6
<p>Comprehensive analysis of drought-related <span class="html-italic">DcbZIP</span> genes. (<b>A</b>) Correlation analysis of 33 upregulated <span class="html-italic">DcbZIP</span> genes. Red indicates a positive correlation and blue indicates a negative correlation. The circle size indicates the absolute value of the correlation coefficient. (<b>B</b>) Co-expression network analysis. The red lines represent a positive correlation. The size represents the degree calculated by the Cytoscape. The four polygons situated in the center represent core genes with high connectivity.</p> "> Figure 7
<p>Interaction networks of the DcbZIPs in <span class="html-italic">D. catenatum</span> and their orthologs in <span class="html-italic">Arabidopsis</span>. The network was predicted by STRING. The DcbZIP proteins were shown in the red font below with the <span class="html-italic">Arabidopsis</span> orthologs in the red dashed box. Empty nodes represent proteins with unknown 3D structures. Filled nodes represent known or predicted 3D structures. Light blue lines and rose lines represent known interactions. Green, orange and blue lines represent predicted interactions. Cyan lines represent text mining, black lines represent co-expression and light purple lines represent protein homology.</p> "> Figure 8
<p>Real-time quantitative PCR analyses of the 17 core <span class="html-italic">DcbZIP</span> genes under drought stress in roots, stems and leaves. The mean expression value was calculated from three replicates. Vertical bars indicate the standard deviation. Values of 0, 3, 6, 9, 12, 24 and 48 indicate hours after treatment. Mean values and standard deviations were calculated according to the data. The unstressed level (0 h) was used as a control. Asterisks (* or **) indicate a significant difference at <span class="html-italic">p</span> < 0.05 or <span class="html-italic">p</span> < 0.01, respectively.</p> ">
Abstract
:1. Introduction
2. Materials and Methods
2.1. Identification of the bZIP Family Members of D. catenatum
2.2. Phylogenetic Analysis of bZIP Proteins
2.3. Analysis of Gene Structure, Conserved Motifs, and Promoter Cis-Regulatory Elements
2.4. Spatial Expression Profile Analysis Using RNA-Seq Data
2.5. Stress Treatments
2.6. Gene Expression Analysis under Drought Treatment
2.7. Analysis of Co-Expression and Protein–Protein Interaction Networks of DcbZIP Proteins
3. Results
3.1. Identification and Physicochemical Properties of bZIP Family in D. catenatum
3.2. Phylogenetic Analysis of bZIP Proteins
3.3. Conserved Motif and Gene Structure of bZIP Family Genes
3.4. Cis-Element Analysis of bZIP Gene Promoters in D. catenatum
3.5. Tissue-Specific Expression Profile of DcbZIP Gene Based on RNA-Seq
3.6. DcbZIP Gene Expression under Drought Stress Based on RNA-Seq
3.7. Analysis of Drought-Related DcbZIP Genes
3.8. Expression Profile Analysis of 17 Core DcbZIP Genes under Drought Stress Using RT-qPCR
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Gene Name | Gene ID | Locus | Length | MW(kDa) | pI | Subcellular Localization | Group |
---|---|---|---|---|---|---|---|
DcbZIP1 | LOC110102063 | NW_021318745.1:471271…486572 | 153 | 16.97 | 9.98 | nuclear | H |
DcbZIP2 | LOC110094784 | NW_021319121.1:1711930…1713378 | 254 | 28.36 | 6.6 | nuclear | E |
DcbZIP3 | LOC110115573 | NW_021320155.1:215…1462 | 155 | 17.66 | 9.03 | nuclear | S |
DcbZIP4 | LOC110112903 | NW_021359921.1: 258…816 | 138 | 15.59 | 11.53 | nuclear | S |
DcbZIP5 | LOC110095238 | NW_021319911.1:476590…477012 | 140 | 15.67 | 11.58 | nuclear | S |
DcbZIP6 | LOC110113945 | NW_021318751.1:434550…435351 | 146 | 16.76 | 10.47 | nuclear | S |
DcbZIP7 | LOC110114248 | NW_021318952.1:1141827…1142966 | 149 | 17.16 | 11.09 | nuclear | S |
DcbZIP8 | LOC110109372 | NW_021318890.1:45595…46690 | 130 | 15.24 | 8.49 | nuclear | S |
DcbZIP9 | LOC110095100 | NW_021319641.1:962641…966712 | 356 | 38.76 | 5.18 | nuclear | C |
DcbZIP10 | LOC110099409 | NW_021319484.1:1588342…1604864 | 311 | 34.37 | 5.57 | nuclear | C |
DcbZIP11 | LOC110116565 | NW_021394673.1:450792…454576 | 317 | 35.95 | 6.49 | mitochondrial | S |
DcbZIP12 | LOC110098756 | NW_021319202.1:1038678…1046470 | 338 | 38.28 | 9.30 | nuclear | A |
DcbZIP13 | LOC110100055 | NW_021319455.1:997836…1000675 | 222 | 24.82 | 5.91 | nuclear | A |
DcbZIP14 | LOC110112185 | NW_021318640.1:185732…187053 | 265 | 28.71 | 9.30 | mitochondrial | A |
DcbZIP15 | LOC110115326 | NW_021319048.1:847890…872251 | 406 | 42.69 | 9.13 | cytoplasmic | A |
DcbZIP16 | LOC110096541 | NW_021319431.1:31825…50187 | 409 | 43.33 | 6.33 | nuclear | G |
DcbZIP17 | LOC110099255 | NW_021319682.1:13603178…13607863 | 683 | 74.16 | 6.38 | nuclear | B |
DcbZIP18 | LOC110104466 | NW_021319842.1:67813…111270 | 398 | 43.50 | 6.16 | nuclear | I |
DcbZIP19 | LOC110116528 | NW_021319455.1:2008465…2012390 | 259 | 28.90 | 6.41 | nuclear | E |
DcbZIP20 | LOC110113515 | NW_021320183.1:270501…301718 | 466 | 51.39 | 6.36 | nuclear | D |
DcbZIP21 | LOC110096667 | NW_021319983.1:403141…412564 | 489 | 54.63 | 5.71 | nuclear | D |
DcbZIP22 | LOC110113543 | NW_021320019.1:9020891…9022087 | 167 | 18.71 | 8.66 | nuclear | S |
DcbZIP23 | LOC110102116 | NW_021318705.1:1911115…1924234 | 273 | 29.49 | 5.94 | nuclear | D |
DcbZIP24 | LOC110110500 | NW_021319360.1:1021557…1023609 | 321 | 36.95 | 5.29 | nuclear | F |
DcbZIP25 | LOC110109220 | NW_021319982.1:676693…690196 | 362 | 39.53 | 5.89 | nuclear | C |
DcbZIP26 | LOC110091873 | NW_021319588.1:431917…450124 | 427 | 47.22 | 6.82 | nuclear | D |
DcbZIP27 | LOC110102106 | NW_021318705.1:1988364…1989735 | 162 | 18.00 | 9.76 | nuclear | A |
DcbZIP28 | LOC110096161 | NW_021318623.1:23442…27784 | 692 | 74.94 | 6.08 | nuclear | B |
DcbZIP29 | LOC110116680 | NW_021319255.1:1051643…1056686 | 542 | 59.41 | 6.21 | nuclear | I |
DcbZIP30 | LOC110099156 | NW_021318726.1:1712729…1719118 | 522 | 56.71 | 6.21 | nuclear | I |
DcbZIP31 | LOC110102661 | NW_021319579.1:559884…583214 | 350 | 38.19 | 6.88 | nuclear | I |
DcbZIP32 | LOC110106152 | NW_021318595.1:5943723…5946939 | 226 | 25.65 | 11.36 | nuclear | S |
DcbZIP33 | LOC110096611 | NW_021319126.1:383344…398145 | 339 | 37.15 | 6.13 | nuclear | I |
DcbZIP34 | LOC110103109 | NW_021320146.1:675175…678827 | 319 | 34.65 | 5.90 | nuclear | E |
DcbZIP35 | LOC110098225 | NW_021318839.1:350918…367871 | 311 | 34.83 | 9.50 | nuclear | A |
DcbZIP36 | LOC110092531 | NW_021318711.1:1796647…1806328 | 396 | 42.68 | 9.19 | nuclear | A |
DcbZIP37 | LOC110109339 | NW_021318998.1:251776…260296 | 407 | 43.50 | 7.70 | nuclear | A |
DcbZIP38 | LOC110097322 | NW_021319772.1:217773…219884 | 141 | 15.69 | 7.65 | nuclear | S |
DcbZIP39 | LOC110114883 | NW_021318595.1:12862132…12864684 | 357 | 38.96 | 7.60 | nuclear | A |
DcbZIP40 | LOC110107968 | NW_021319536.1:408463…445084 | 277 | 30.19 | 5.19 | nuclear | A |
DcbZIP41 | LOC110095320 | NW_021318963.1:1120306…1130172 | 359 | 38.07 | 7.11 | nuclear | G |
DcbZIP42 | LOC110094070 | NW_021318618.1:1794449…1795054 | 159 | 18.31 | 7.07 | nuclear | S |
DcbZIP43 | LOC110109278 | NW_021416702.1:86653…87395 | 183 | 21.41 | 6.72 | nuclear | S |
DcbZIP44 | LOC110099470 | NW_021318619.1:750999…751924 | 132 | 15.65 | 10.09 | nuclear | S |
DcbZIP45 | LOC110110747 | NW_021318796.1:2352740…2370581 | 427 | 47.26 | 8.46 | nuclear | D |
DcbZIP46 | LOC110094737 | NW_021319121.1:686641…695563 | 365 | 40.63 | 7.06 | nuclear | D |
DcbZIP47 | LOC110110388 | NW_021319315.1:2104944…2125602 | 381 | 42.91 | 7.68 | nuclear | D |
DcbZIP48 | LOC110094083 | NW_021318700.1:245031…246643 | 146 | 16.34 | 8.71 | nuclear | H |
DcbZIP49 | LOC110091793 | NW_021318565.1:363970…370844 | 447 | 50.01 | 7.32 | nuclear | D |
DcbZIP50 | LOC110112805 | NW_021318937.1:66248…73259 | 433 | 48.47 | 7.75 | nuclear | D |
DcbZIP51 | LOC110105751 | NW_021318677.1:122368…135356 | 341 | 37.24 | 6.22 | nuclear | I |
DcbZIP52 | LOC110114853 | NW_021319083.1:8027963…8050443 | 394 | 42.69 | 5.44 | nuclear | I |
DcbZIP53 | LOC110099371 | NW_021319442.1:514414…515591 | 143 | 16.69 | 8.85 | nuclear | S |
DcbZIP54 | LOC110109693 | NW_021378092.1:460796…469115 | 386 | 41.58 | 5.14 | nuclear | G |
DcbZIP55 | LOC110094315 | NW_021319161.1:846164…858315 | 269 | 30.97 | 8.75 | nuclear | G |
DcbZIP56 | LOC110101858 | NW_021319436.1:2509122…2519085 | 161 | 18.07 | 9.44 | nuclear | H |
DcbZIP57 | LOC110111774 | NW_021318920.1:351221…358735 | 369 | 41.59 | 5.68 | nuclear | D |
DcbZIP58 | LOC110100891 | NW_021318787.1:716526…717410 | 130 | 15.24 | 8.49 | nuclear | S |
DcbZIP59 | LOC110095296 | NW_021319910.1:646885…655651 | 401 | 44.12 | 5.79 | nuclear | I |
DcbZIP60 | LOC110113665 | NW_021324968.1:31584…34398 | 335 | 37.95 | 5.13 | nuclear | B |
DcbZIP61 | LOC110101931 | NW_021319436.1:1660963…1677531 | 361 | 39.45 | 8.47 | nuclear | I |
DcbZIP62 | LOC110106828 | NW_021319013.1:318529…320289 | 273 | 29.15 | 9.73 | nuclear | A |
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Wang, P.; Li, Y.; Zhang, T.; Kang, Y.; Li, W.; Wang, J.; Yu, W.; Zhou, Y. Identification of the bZIP Gene Family and Investigation of Their Response to Drought Stress in Dendrobium catenatum. Agronomy 2023, 13, 236. https://doi.org/10.3390/agronomy13010236
Wang P, Li Y, Zhang T, Kang Y, Li W, Wang J, Yu W, Zhou Y. Identification of the bZIP Gene Family and Investigation of Their Response to Drought Stress in Dendrobium catenatum. Agronomy. 2023; 13(1):236. https://doi.org/10.3390/agronomy13010236
Chicago/Turabian StyleWang, Peng, Yuxin Li, Tingting Zhang, Yuqian Kang, Wei Li, Jian Wang, Wengang Yu, and Yang Zhou. 2023. "Identification of the bZIP Gene Family and Investigation of Their Response to Drought Stress in Dendrobium catenatum" Agronomy 13, no. 1: 236. https://doi.org/10.3390/agronomy13010236