Identification and Characterization of Wall-Associated Kinase (WAK) and WAK-like (WAKL) Gene Family in Juglans regia and Its Wild Related Species Juglans mandshurica
Abstract
:1. Introduction
2. Materials and Methods
2.1. Identification of WAK/WAKL Members in J. regia and Its Wild Related Species J. mandshurica
2.2. Chromosome Localization and Gene Duplication Mode Analysis
2.3. Physicochemical Properties and Subcellular Localization Prediction
2.4. Phylogenetic Tree Construction and Gene Structure Analysis
2.5. Cis-Acting Element Prediction and Gene Expression Analysis
3. Results
3.1. Genome-Wide Identification and Phylogenetic Analysis of the WAK/WAKL Gene Family in J. regia and Its Wild Related Species J. mandshurica
3.2. Physicochemical Property and Subcellular Localization Analysis of the WAK/WAKL Proteins in J. regia and Its Wild Related Species J. mandshurica
3.3. Protein Domain and Gene Structure Analysis of the WAK/WAKL Members in J. regia and Its Wild Related Species J. mandshurica
3.4. Chromosomal Distribution and Duplication Mode Analysis of the WAK/WAKL Gene Family in J. regia and Its Wild Related Species J. mandshurica
3.5. Collinearity and Selective Pressure Analysis of the WAK/WAKL Members in J. regia and Its Wild Related Species J. mandshurica
3.6. Cis-Acting Elements Analysis of Promoters of WAK/WAKL Genes in J. regia and Its Wild Related Species J. mandshurica
3.7. Expression Profile Analysis of the WAK/WAKL Genes in J. regia and Its Wild Related Species J. mandshurica
4. Discussion
4.1. Characteristics of WAK/WAKL Genes in J. regia and J. mandshurica
4.2. The Tandem Duplication of the WAK/WAKL Gene Family in J. regia and J. mandshurica
4.3. The Conserved Domain, Gene Structure, and cis-Acting Elements of the WAK/WAKL Genes in J. regia and J. mandshurica
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 | No. of Amino Acids | Mol. Wt (kDa) | Isoelectric Point (pI) | Instability Index (II) | Aliphatic Index | Grand Average of Hydropathicity (GRAVY) | Subcellular Localizationa |
---|---|---|---|---|---|---|---|
JrWAK1 | 690 | 77,758.55 | 5.97 | 40.56 | 80.94 | −0.31 | plas |
JrWAK2 | 839 | 91,544.55 | 6.36 | 33.11 | 82.81 | −0.33 | plas |
JrWAK3 | 778 | 85,990.06 | 6.36 | 37.49 | 92.57 | −0.19 | vacu |
JrWAK4 | 836 | 92,128.95 | 6.67 | 35.95 | 83.83 | −0.29 | plas |
JrWAK5 | 778 | 85,292.05 | 6.25 | 31.33 | 87.90 | −0.21 | vacu |
JrWAK6 | 768 | 85,036.38 | 6.96 | 37.39 | 91.76 | −0.19 | plas |
JrWAK7 | 716 | 79,111.38 | 8.12 | 34.46 | 89.15 | −0.26 | vacu |
JrWAK8 | 713 | 79,985.06 | 5.93 | 36.64 | 83.52 | −0.22 | vacu |
JrWAK9 | 713 | 79,776.70 | 5.64 | 33.72 | 82.85 | −0.24 | vacu |
JrWAK10 | 763 | 84,326.97 | 5.43 | 36.41 | 84.84 | −0.20 | plas |
JrWAK11 | 707 | 78,434.90 | 8.48 | 42.21 | 87.96 | −0.21 | plas |
JrWAKL1 | 673 | 74,644.43 | 5.27 | 43.53 | 87.74 | −0.16 | extr |
JrWAKL2 | 708 | 79,775.49 | 7.86 | 38.86 | 84.66 | −0.23 | chlo |
JrWAKL3 | 739 | 83,259.24 | 7.71 | 36.16 | 84.79 | −0.26 | extr |
JrWAKL4 | 644 | 70,964.82 | 8.83 | 37.45 | 92.34 | −0.13 | vacu |
JrWAKL5 | 827 | 91,687.81 | 7.63 | 36.59 | 90.50 | −0.16 | plas |
JrWAKL6 | 694 | 76,326.10 | 5.56 | 36.81 | 83.16 | −0.18 | plas |
JrWAKL7 | 707 | 78,717.69 | 6.33 | 32.77 | 86.53 | −0.14 | plas |
JrWAKL8 | 723 | 81,305.71 | 6.01 | 33.79 | 81.29 | −0.23 | plas |
JrWAKL9 | 513 | 57,573.86 | 7.82 | 27.57 | 86.80 | −0.08 | chlo |
JrWAKL10 | 705 | 79,273.50 | 6.54 | 28.82 | 85.97 | −0.18 | plas |
JrWAKL11 | 603 | 67,641.00 | 7.76 | 31.67 | 82.12 | −0.35 | nucl |
JrWAKL12 | 681 | 76,621.84 | 6.37 | 48.65 | 83.85 | −0.33 | plas |
JrWAKL13 | 678 | 75,503.57 | 5.91 | 43.32 | 82.05 | −0.24 | chlo |
JrWAKL14 | 787 | 87,360.88 | 6.51 | 33.75 | 83.60 | −0.23 | plas |
JrWAKL15 | 669 | 74,597.36 | 5.94 | 39.87 | 81.46 | −0.22 | vacu |
JrWAKL16 | 670 | 74,773.49 | 7.78 | 46.52 | 82.19 | −0.30 | plas |
JmWAK1 | 758 | 84,080.04 | 6.35 | 35.01 | 84.37 | −0.21 | plas |
JmWAK2 | 749 | 83,946.50 | 5.86 | 35.86 | 82.26 | −0.26 | vacu |
JmWAK3 | 1396 | 155,950.00 | 7.06 | 38.40 | 87.49 | −0.25 | plas |
JmWAK4 | 763 | 84,642.55 | 7.88 | 40.86 | 86.09 | −0.27 | plas |
JmWAK5 | 779 | 85,485.49 | 6.56 | 35.61 | 88.19 | −0.22 | plas |
JmWAKL1 | 629 | 69,698.84 | 6.64 | 51.86 | 94.10 | 0.01 | plas |
JmWAKL2 | 632 | 69,194.91 | 6.20 | 36.32 | 87.66 | −0.16 | plas |
JmWAKL3 | 1182 | 133,611.68 | 6.61 | 32.72 | 88.15 | −0.22 | plas |
JmWAKL4 | 881 | 99,728.80 | 6.22 | 35.90 | 85.27 | −0.23 | chlo |
JmWAKL5 | 706 | 78,535.72 | 4.86 | 36.53 | 83.81 | −0.21 | plas |
JmWAKL6 | 682 | 78,128.27 | 5.79 | 52.94 | 83.05 | −0.22 | plas |
JmWAKL7 | 880 | 98,454.69 | 8.40 | 39.81 | 90.69 | −0.23 | plas |
JmWAKL8 | 662 | 73,877.35 | 7.11 | 42.40 | 88.34 | −0.30 | plas |
JmWAKL9 | 959 | 106,500.53 | 5.56 | 40.59 | 95.62 | −0.14 | plas |
Gene Name | Whole Genome Duplication (WGD) | Tandem Duplication (TD) | Dispersed Duplication (DSD) | Proximal Duplication (PD) |
---|---|---|---|---|
JrWAK1 | √ | |||
JrWAK2 | √ | |||
JrWAK3 | √ | |||
JrWAK4 | √ | |||
JrWAK5 | √ | |||
JrWAK6 | √ | |||
JrWAK7 | √ | |||
JrWAK8 | √ | |||
JrWAK9 | √ | |||
JrWAK10 | √ | √ | ||
JrWAK11 | √ | |||
JrWAKL1 | ||||
JrWAKL2 | √ | |||
JrWAKL3 | √ | |||
JrWAKL4 | √ | |||
JrWAKL5 | √ | |||
JrWAKL6 | √ | √ | ||
JrWAKL7 | √ | |||
JrWAKL8 | √ | |||
JrWAKL9 | √ | |||
JrWAKL10 | √ | |||
JrWAKL11 | √ | |||
JrWAKL12 | √ | |||
JrWAKL13 | √ | |||
JrWAKL14 | √ | |||
JrWAKL15 | ||||
JrWAKL16 | √ | |||
JmWAK1 | √ | |||
JmWAK2 | √ | |||
JmWAK3 | √ | |||
JmWAK4 | √ | |||
JmWAK5 | √ | |||
JmWAKL1 | √ | |||
JmWAKL2 | √ | |||
JmWAKL3 | √ | |||
JmWAKL4 | √ | |||
JmWAKL5 | √ | |||
JmWAKL6 | √ | |||
JmWAKL7 | √ | |||
JmWAKL8 | √ | |||
JmWAKL9 | √ |
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Li, M.; Ma, J.; Liu, H.; Ou, M.; Ye, H.; Zhao, P. Identification and Characterization of Wall-Associated Kinase (WAK) and WAK-like (WAKL) Gene Family in Juglans regia and Its Wild Related Species Juglans mandshurica. Genes 2022, 13, 134. https://doi.org/10.3390/genes13010134
Li M, Ma J, Liu H, Ou M, Ye H, Zhao P. Identification and Characterization of Wall-Associated Kinase (WAK) and WAK-like (WAKL) Gene Family in Juglans regia and Its Wild Related Species Juglans mandshurica. Genes. 2022; 13(1):134. https://doi.org/10.3390/genes13010134
Chicago/Turabian StyleLi, Mengdi, Jiayu Ma, Hengzhao Liu, Mengwei Ou, Hang Ye, and Peng Zhao. 2022. "Identification and Characterization of Wall-Associated Kinase (WAK) and WAK-like (WAKL) Gene Family in Juglans regia and Its Wild Related Species Juglans mandshurica" Genes 13, no. 1: 134. https://doi.org/10.3390/genes13010134
APA StyleLi, M., Ma, J., Liu, H., Ou, M., Ye, H., & Zhao, P. (2022). Identification and Characterization of Wall-Associated Kinase (WAK) and WAK-like (WAKL) Gene Family in Juglans regia and Its Wild Related Species Juglans mandshurica. Genes, 13(1), 134. https://doi.org/10.3390/genes13010134