Genome-Wide Re-Identification and Analysis of CrRLK1Ls in Tomato
Abstract
:1. Introduction
2. Results
2.1. Identification of Tomato CrRLK1L Protein Kinases
2.2. Phylogenetic Analysis of the Tomato CrRLK1L Protein Kinases
2.3. Tomato CrRLK1L Gene Locations and Duplication on Tomato Chromosome
2.4. Tomato CrRLK1L Protein Domain and Gene Structure
2.5. Prediction of SlCrRLK1L Conserved Protein Motifs
2.6. Subcellular Localization
2.7. SlCrRLK1L Gene Promoter Analysis
2.8. SlCrRLK1L Gene Expression Pattern Analysis
3. Discussion
4. Materials and Methods
4.1. Protein Identification and Phylogenetic Analysis
4.2. Antibody Preparation
4.3. Western Blot Assay
4.4. Gene Location and Collinearity Analysis
4.5. Subcellular Localization Analysis
4.6. Protein Domain and Gene Structure Analyses
4.7. Conserved Protein Motif Analysis
4.8. Promoter Analysis
4.9. Gene Expression Pattern Analysis
4.10. Accession Number
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Protein Name | Protein ID in NCBI | Protein Length (aa) | Molecular Weight (Da) | Theoretical pI | GRAVY | Matched SGN Locus | Annotation Difference in NCBI and SGN |
---|---|---|---|---|---|---|---|
SlCrRLK1L1 | XP_025886195.1 | 854 | 95,039.67 | 6.86 | −0.268 | Solyc01g059910 | Y |
SlCrRLK1L2 | XP_004230878.1 | 876 | 96,273.18 | 5.82 | −0.212 | Solyc01g109950 | N |
SlCrRLK1L3 | XP_019067666.1 | 1152 | 129,597.94 | 6.93 | −0.174 | Solyc02g014030 | N |
SlCrRLK1L4 | XP_004233885.1 | 868 | 96,438.64 | 5.49 | −0.28 | Solyc02g069970 | Y |
SlCrRLK1L5 | XP_004233025.1 | 1002 | 112,230.67 | 6.36 | −0.312 | Solyc02g071860 | Y |
SlCrRLK1L6 | XP_010316862.1 | 995 | 111,071.97 | 5.79 | −0.108 | Solyc02g071880 | N |
SlCrRLK1L7 | XP_004232151.1 | 869 | 97,152.91 | 6.14 | −0.234 | Solyc02g089090 | Y |
SlCrRLK1L8 | NP_001234869.1 | 903 | 101,461.32 | 8.92 | −0.197 | Solyc02g091590 | N |
SlCrRLK1L9 | XP_004234657.2 | 817 | 91,323.59 | 5.9 | −0.168 | Solyc03g044160 | Y |
SlCrRLK1L10 | XP_010318169.1 | 865 | 97,835 | 5.41 | −0.201 | Solyc03g093380 | N |
SlCrRLK1L11 | XP_025886103.1 | 1340 | 150,300.63 | 6.39 | −0.226 | Solyc03g115710 | Y |
SlCrRLK1L12 | XP_010318523.1 | 894 | 99,669.44 | 5.49 | −0.16 | Solyc03g121230 | N |
SlCrRLK1L13 | XP_004239170.1 | 926 | 103,366.23 | 5.88 | −0.267 | Solyc05g014240 | N |
SlCrRLK1L14 | XP_004240198.2 | 840 | 92,846.45 | 6.26 | 0.021 | Solyc05g054680 | N |
SlCrRLK1L15 | XP_004239762.1 | 811 | 90,461.22 | 5.66 | −0.079 | Solyc05g054860 | N |
SlCrRLK1L16 | XP_004240568.1 | 887 | 97,458.64 | 5.73 | −0.264 | Solyc06g009540 | N |
SlCrRLK1L17 | XP_004240569.1 | 880 | 97,075.96 | 6.33 | −0.246 | Solyc06g009550 | Y |
SlCrRLK1L18 | XP_004243035.1 | 854 | 94,945.25 | 6.36 | −0.259 | Solyc07g008400 | N |
SlCrRLK1L19 | XP_004246699.1 | 928 | 102,646.36 | 5.82 | −0.212 | Solyc09g007280 | N |
SlCrRLK1L20 | XP_004246282.1 | 889 | 97,348.77 | 5.78 | −0.22 | Solyc09g015830 | Y |
SlCrRLK1L21 | XP_004247083.1 | 904 | 101,257.01 | 5.48 | −0.107 | Solyc09g060110 | N |
SlCrRLK1L22 | XP_010327142.1 | 840 | 91,947.64 | 5.26 | 0.032 | Solyc10g006870 | N |
SlCrRLK1L23 | XP_004248695.3 | 868 | 96,419.44 | 6.09 | −0.221 | Solyc10g054050 | Y |
SlCrRLK1L24 | XP_004251295.1 | 836 | 91,944.54 | 5.84 | −0.1 | Solyc11g072910 | Y |
Species | Number of CrRLK1Ls | Reference |
---|---|---|
Arabidopsis thaliana | 17 | [42] |
Oryza sativa (rice) | 16 | [43] |
Malus domestica (apple) | 74 | [40] |
Fragaria vesca (strawberry) | 62 | [44] |
Citrus sinensis ‘Valencia’ (Citrus) | 47 | [45] |
Glycine max L. (soybean) | 38 | [33] |
Nicotiana tabacum L. (tobacco) | 48 | [34] |
Nicotiana benthamiana | 31 | [46] |
Chenopodium quinoa | 26 | [35] |
Pyrus bretchneideri (pear) | 26 | [32] |
Populus trichocarpa (black cottonwood) | 42 | [47] |
Gossypium raimondii, G. arboreum, and G. hirsutum TM-1 (cotton) | 44 | [48] |
Boea hygrometrica | 18 | [49] |
Solanum tuberosum (potato) | 17 | [50] |
Solanum lycopersicum (tomato) | 24 | This study |
Amborella trichopoda | 9 | [51] |
Marchantia polymorpha | 1 | [52] |
Physcomitrella patens | 6 | [53] |
Selaginella moellendorffii | 2 | [54] |
Picea abies | 7 | [55] |
Closterium peracerosum-strigosumlittorale complex | 1 | [56] |
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Ma, W.; Liu, X.; Chen, K.; Yu, X.; Ji, D. Genome-Wide Re-Identification and Analysis of CrRLK1Ls in Tomato. Int. J. Mol. Sci. 2023, 24, 3142. https://doi.org/10.3390/ijms24043142
Ma W, Liu X, Chen K, Yu X, Ji D. Genome-Wide Re-Identification and Analysis of CrRLK1Ls in Tomato. International Journal of Molecular Sciences. 2023; 24(4):3142. https://doi.org/10.3390/ijms24043142
Chicago/Turabian StyleMa, Wenpeng, Xin Liu, Kai Chen, Xinlong Yu, and Dongchao Ji. 2023. "Genome-Wide Re-Identification and Analysis of CrRLK1Ls in Tomato" International Journal of Molecular Sciences 24, no. 4: 3142. https://doi.org/10.3390/ijms24043142