Identification and Analysis of the EIN3/EIL Gene Family in Populus × xiaohei T. S. Hwang et Liang: Expression Profiling during Stress
<p>The products of PCR amplification of <span class="html-italic">PsnEIN3/EIL</span> gene. The arrow on the left is the band size of the electrophoresis marker. Electrophoresis bands from left to right: DL2000Marker(M); gel electrophoresis imaging bands of <span class="html-italic">PsnEIL2.2</span>, <span class="html-italic">PsnEIL2.3</span>, <span class="html-italic">PsnEIL2.4</span>, <span class="html-italic">PsnEIL2.5</span>, <span class="html-italic">PsnEIL4.1</span>, <span class="html-italic">PsnEIL4.2</span>, <span class="html-italic">PsnEIN3.1</span>, and <span class="html-italic">PsnEIL2.1</span>. The lengths of the <span class="html-italic">PsnEIN3/EIL</span> genes were 1980, 1989, 1989, 1962, 1197, 1788, 1854, and 1539 bp.</p> "> Figure 2
<p>Sequence alignment of all identified EIN3/EIL genes in <span class="html-italic">Populus</span> × <span class="html-italic">xiaohei</span> and <span class="html-italic">A. thaliana</span>. Sequence comparisons were made via alignment using ClustaW, and identical or similar residues are shaded in different background colors. The areas with 100% similarity are displayed in black, pink indicates similarity of 75%, and blue indicates similarity of 50%. The approximate position of the EIN3 structural domain is shown as a red line above the matched sequences. Amino acid enrichment regions are indicated by black lines below the matched sequences: AD: acidic amino acid enrichment region; BDⅠ–V: basic amino acid enrichment regionⅠ–V; PR: proline enrichment region.</p> "> Figure 3
<p>Phylogenetic relationships of EIN3/EIL genes of <span class="html-italic">Populus</span> × <span class="html-italic">xiaohei</span> and other species. The phylogenetic tree was generated from the alignment of 30 EIN3/EIL protein homeodomain sequences with 1000 bootstrap replicates. EIN3/EIL members are distributed in three main clades, namely clades A, B, and C marked in green, blue, and yellow, respectively. Bootstrap values are shown near the nodes. (At: <span class="html-italic">Arabidopsis thaliana</span> [<span class="html-italic">AtEIN3</span> (NP_188713.1), <span class="html-italic">AtEIL1</span> (NP_180273.1), <span class="html-italic">AtEIL2</span> (NP_001332194.1), <span class="html-italic">AtEIL3</span> (NP_177514.1), <span class="html-italic">AtEIL4</span> (NP_20131.1), <span class="html-italic">AtEIL5</span> (NP_196574)]; Tc: <span class="html-italic">Theobroma Cacao</span> [<span class="html-italic">TcEIN3</span> (EOY34301.1), <span class="html-italic">TcEIL3</span> (XP_017982625.1), <span class="html-italic">TcEIL4</span> (EOX92159.1)]; Os: <span class="html-italic">Oryza sativa</span> [<span class="html-italic">OsEIL1</span> (XP_015629857.1), <span class="html-italic">OsEIL2</span> (XP_015646574.1), <span class="html-italic">OsEIL3</span> (XP_015648717.1), <span class="html-italic">OsEIL4</span> (XP_015625091.1), <span class="html-italic">OsEIL5</span> (CAD40887.2), <span class="html-italic">OsEIL6</span> (XP_015612094.1)]; Ac: <span class="html-italic">Actinidia chinensis</span> [<span class="html-italic">AcEIL1</span> (PSS14564.1), <span class="html-italic">AcEIL2</span> (PSS14565.1), <span class="html-italic">AcEIL3</span> (ACJ70676.1), <span class="html-italic">AcEIL4</span> (PSR86855.1), <span class="html-italic">AcEIL5</span> (PSS21513.1)]; Zm: <span class="html-italic">Zea Mays</span> [<span class="html-italic">ZmEIL5</span> (KJ726967.1), <span class="html-italic">ZmEIL6</span> (KJ728014.1)]; Cm: <span class="html-italic">Cmaris Melo</span> [<span class="html-italic">CmEIL2</span> (NW_007546307.1)]).</p> "> Figure 4
<p>Analysis of the conserved motifs of <span class="html-italic">EIN3/EIL</span> genes in <span class="html-italic">Populus</span> × <span class="html-italic">xiaohei</span> and <span class="html-italic">A. thaliana</span>. Structural features of EIN3/EIL transcription factors in <span class="html-italic">Populus</span> × <span class="html-italic">xiaohei</span> and <span class="html-italic">A. thaliana</span>. (<b>A</b>) The NJ tree and motif analysis were constructed from a total of 14 EIN3/EIL genes from <span class="html-italic">Populus</span> × <span class="html-italic">xiaohei</span> and <span class="html-italic">A. thaliana</span>. The numbers below the motifs correspond to their approximate position and length in the residue. The EIN3 domain is located in the first half of the protein, between approximately 80 and 280 residues. (<b>B</b>) LOGO of 10 conservative motifs was predicted by the MEME tool.</p> "> Figure 5
<p>Chromosomal location of <span class="html-italic">PsnEIN3/EIL</span> genes. EIN3/EIL genes were mapped to different poplar chromosomes using the MapGene2Chrom tool. Gene positions on chromosomes are as follows: Chr01:1163628-1167197, Chr03:20939782-20943057, Chr04:20998609-21002260, Chr08:626991-631538, and Chr10:22117935e22122336). Chr represents the chromosome. The rule on the left indicates the physical map distance among genes (Mbp).</p> "> Figure 6
<p>Genome-wide synteny analysis of <span class="html-italic">PsnEIN3/EIL</span> genes. chr1–19 represent chromosomes in <span class="html-italic">Populus</span> × <span class="html-italic">xiaohei</span>. All identified EIN3/EIL genes were mapped onto corresponding chromosomes. The red lines link the syntenic paralogs.</p> "> Figure 7
<p>Synteny analysis of EIN3/EIL genes between <span class="html-italic">Populus</span> × <span class="html-italic">xiaohei</span> and other plants. (<b>A</b>) Dicotyledonous plant <span class="html-italic">A. thaliana</span>. (<b>B</b>) Dicotyledonous plant <span class="html-italic">G. max</span>. (<b>C</b>) Dicotyledonous plant <span class="html-italic">M. pumila</span>. Gray lines in the background indicate collinear blocks within <span class="html-italic">Populus</span> × <span class="html-italic">xiaohei</span> and other plant genomes; red lines indicate syntenic EIN3/EIL gene pairs.</p> "> Figure 8
<p>Tissue-specific expression pattern of <span class="html-italic">PsnEIN3/EIL</span> genes. The heat map shows the relative expression levels of EIN3/EIL genes in different plant parts (roots, xylem, phloem, third leaves, and terminal buds) of <span class="html-italic">Populus</span> × <span class="html-italic">xiaohei</span>.</p> "> Figure 9
<p><span class="html-italic">PsnEIN3/EIL</span> gene expression patterns in different stem segments of <span class="html-italic">Populus</span> × <span class="html-italic">xiaohei</span>. Heat map showing the expression levels of the <span class="html-italic">PsnEIN3/EIL</span> genes in different stem segments. The first stem segment (1st) to the eleventh stem segment (11th) are presented in abbreviated form.</p> "> Figure 10
<p>Relative <span class="html-italic">PsnEIN3/EIL</span> gene expression patterns in different leaves of <span class="html-italic">Populus</span> × <span class="html-italic">xiaohei</span>. Heat map showing the expression levels of <span class="html-italic">PsnEIN3/EIL</span> genes in different leaf developmental stages. The first leaf (1st) to the fourteenth leaf (14th) are presented in abbreviated form.</p> "> Figure 11
<p><span class="html-italic">EIN3/EIL</span> gene expression patterns of <span class="html-italic">Populus</span> × <span class="html-italic">xiaohei</span> under Nacl stress. Heat map showing the relative expression levels of <span class="html-italic">PsnEIN3/EIL</span> genes during salt damage treatment. sqRT-PCR was used to measure the transcription levels in root and leaf samples under stress treatment, and the data were normalized. (<b>A</b>) Roots. (<b>B</b>) Leaf. The color scale on the right of the heat map indicates the expression level: red indicates upregulation, and blue indicates downregulation.</p> "> Figure 12
<p><span class="html-italic">EIN3/EIL</span> gene expression patterns of <span class="html-italic">Populus</span> × <span class="html-italic">xiaohei</span> under CdCl<sub>2</sub> stress. (<b>A</b>) Root. (<b>B</b>) Leaf.</p> "> Figure 12 Cont.
<p><span class="html-italic">EIN3/EIL</span> gene expression patterns of <span class="html-italic">Populus</span> × <span class="html-italic">xiaohei</span> under CdCl<sub>2</sub> stress. (<b>A</b>) Root. (<b>B</b>) Leaf.</p> "> Figure 13
<p><span class="html-italic">EIN3/EIL</span> gene expression patterns of <span class="html-italic">Populus</span> × <span class="html-italic">xiaohei</span> under NaHCO<sub>3</sub> stress. (<b>A</b>) Root. (<b>B</b>) Leaf.</p> "> Figure 14
<p><span class="html-italic">EIN3/EIL</span> gene expression patterns of <span class="html-italic">Populus</span> × <span class="html-italic">xiaohei</span> under PEG stress. (<b>A</b>) Root. (<b>B</b>) Leaf.</p> "> Figure 15
<p>EIN3/EIL gene expression patterns of <span class="html-italic">Populus</span> × <span class="html-italic">xiaohei</span> under ABA stress.</p> ">
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material
2.2. Cloning of PsnEIN3/EIL Genes of Populus × xiaohei
2.3. Bioinformatic Analysis
2.4. Semi-Quantitative Reverse Transcription PCR, (sqRT-PCR)
3. Results and Analysis
3.1. Cloning and Identification of EIN3/EIL Gene Sequences of Populus × xiaohei
3.2. Bioinformatic Analysis of the EIN3/EIL Gene of Populus × xiaohei
3.2.1. Analysis of the Physicochemical Properties of PsnEIN3/EIL Gene in Populus × xiaohei
3.2.2. Multiple Sequence Alignment of PsnEIN3/EIL Proteins
3.2.3. Phylogenetic Analysis of PsnEIN3/EIL Genes in Populus × xiaohei
3.2.4. Analysis of Conserved Motifs Analysis of EIN3/EIL Proteins
3.2.5. Chromosomal Location, Duplication Analysis, and Ka/Ks Calculation
3.3. Gene Expression Pattern Analysis of EIN3/EIL Genes
3.3.1. Characterization of Tissue Expression of PsnEIN3/EIL in Populus × xiaohei
3.3.2. PsnEIN3/EIL Genes Showed Different Expression Patterns during the Development of Stems of Populus × xiaohei
3.3.3. Most PsnEIN3/EIL Genes Are Involved in the Maturation and Senescence Processes of Leaves
3.3.4. The PsnEIN3/EIL Gene of Populus × xiaohei Could Be Induced by High Salt Concentrations
3.3.5. Involvement of PsnEIN3/EIL in the Response to Heavy Metal Stress in Populus × xiaohei
3.3.6. Response of PsnEIN3/EIL Genes to NaHCO3 in Populus × xiaohei
3.3.7. Response of PsnEIN3/EIL Genes to PEG in Populus × xiaohei
3.3.8. The PsnEIN3/EIL Genes were Involved in the Abscisic Acid Response of Populus × xiaohei
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 | Chromosome | ORF Length | Protein Length /Amino Acids | PI | Molecular Weight (Da) | Subcellular Localization |
---|---|---|---|---|---|---|
PsnEIN3.1 | Chr04 | 1854 | 617 | 5.68 | 70,025.84 | Nucleus |
PsnEIL2.1 | Chr10 | 1539 | 556 | 5.97 | 62,939.99 | Nucleus |
PsnEIL2.2 | Chr10 | 1980 | 659 | 5.49 | 74,463.65 | Nucleus |
PsnEIL2.3 | Chr08 | 1989 | 662 | 5.28 | 74,991.26 | Nucleus |
PsnEIL2.4 | Chr08 | 1989 | 662 | 5.29 | 74,934.21 | Nucleus |
PsnEIL2.5 | Chr08 | 1962 | 653 | 5.38 | 73,785.89 | Nucleus |
PsnEIL4.1 | Chr01 | 1197 | 398 | 8.24 | 44,013.25 | Nucleus |
PsnEIL4.2 | Chr03 | 1788 | 595 | 5.60 | 66,742.84 | Nucleus |
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Liu, Y.; Jin, C.; Li, Y.; Wang, L.; Li, F.; Wang, B.; Jiang, J.; Zheng, Z.; Li, H. Identification and Analysis of the EIN3/EIL Gene Family in Populus × xiaohei T. S. Hwang et Liang: Expression Profiling during Stress. Forests 2022, 13, 382. https://doi.org/10.3390/f13030382
Liu Y, Jin C, Li Y, Wang L, Li F, Wang B, Jiang J, Zheng Z, Li H. Identification and Analysis of the EIN3/EIL Gene Family in Populus × xiaohei T. S. Hwang et Liang: Expression Profiling during Stress. Forests. 2022; 13(3):382. https://doi.org/10.3390/f13030382
Chicago/Turabian StyleLiu, Yuting, Chunhui Jin, Yue Li, Lili Wang, Fangrui Li, Bo Wang, Jing Jiang, Zhimin Zheng, and Huiyu Li. 2022. "Identification and Analysis of the EIN3/EIL Gene Family in Populus × xiaohei T. S. Hwang et Liang: Expression Profiling during Stress" Forests 13, no. 3: 382. https://doi.org/10.3390/f13030382