Genome-Wide Identification, Diversification, and Expression Analysis of Lectin Receptor-Like Kinase (LecRLK) Gene Family in Cucumber under Biotic Stress
Abstract
:1. Introduction
2. Results
2.1. Identification and Physicochemical Properties of CsaLecRLK Genes
2.2. Phylogenetic Relationship, Motif Composition and Gene Structure Analysis of CsaLecRLKs Genes
2.3. Chromosomal Location and Gene Duplication Analysis of CsaLecRLK Genes
2.4. Gene Ontology (GO) and Promoter Analysis of CsaLecRLK Genes
2.5. Subcellular Localization of CsaLecRLKs
2.6. Expression Pattern and qRT-PCR Validation of CsaLecRLK Genes
3. Discussion
4. Materials and Methods
4.1. Identification and Sequence Retrieval for CsaLecRLK
4.2. Phylogenetic Analysis of CsaLecRLK
4.3. Ka/Ks for Duplicated CsaLecRLK Genes and Their Rate of Divergence
4.4. Conserved Motifs, Exon-Intron Structure Analysis, and Physicochemical Parameters of CsaLecRLK Proteins
4.5. Cis-Elements Predictions of CsaLecRLK
4.6. Chromosomal Location and Syntenic Relationship, and Gene Onotology Enrichment Analysis
4.7. Subcellular Localization of CsaLecRLKs
4.8. Plant Materials and Treatment
4.9. Seed Priming with PGPF-Trichoderma Harzianum Isolate (TriH_JSB27)
4.10. RNA Isolation and Expression Profiling of C. sativus under Biotic Stress
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene 1 | Gene 2 | Ks | Ka | Ka/Ks | Divergence Time | Selection Pressure | Gene Duplications |
---|---|---|---|---|---|---|---|
Between L-type genes | |||||||
CsaLecRLK1 | CsaLecRLK5 | 1.19 | 0.40 | 0.33 | 39.67 | Purifying Selection | WGD or Segmental |
CsaLecRLK14 | CsaLecRLK16 | 0.91 | 0.53 | 0.58 | 30.33 | Purifying Selection | WGD or Segmental |
CsaLecRLK2 | CsaLecRLK4 | 0.51 | 0.55 | 1.09 | 17.00 | Positive Selection | Tandem |
CsaLecRLK6 | CsaLecRLK7 | 0.34 | 0.38 | 1.10 | 11.33 | Positive Selection | Tandem |
CsaLecRLK18 | CsaLecRLK19 | 0.18 | 0.28 | 1.55 | 6.00 | Positive Selection | Tandem |
CsaLecRLK22 | CsaLecRLK23 | 0.52 | 0.14 | 0.26 | 17.33 | Purifying Selection | Tandem |
CsaLecRLK8 | CsaLecRLK9 | 0.79 | 0.38 | 0.48 | 26.33 | Purifying Selection | Dispersed |
CsaLecRLK10 | CsaLecRLK13 | 0.84 | 0.55 | 0.65 | 28.00 | Purifying Selection | Dispersed |
CsaLecRLK20 | CsaLecRLK21 | 1.73 | 0.30 | 0.17 | 57.67 | Purifying Selection | Dispersed |
CsaLecRLK3 | CsaLecRLK11 | 0.89 | 0.59 | 0.67 | 29.67 | Purifying Selection | Proximal |
CsaLecRLK12 | CsaLecRLK17 | 0.85 | 0.61 | 0.72 | 28.33 | Purifying Selection | Proximal |
Between G-type genes | |||||||
CsaLecRLK2 | CsaLecRLK3 | 0.22 | 0.41 | 1.85 | 7.33 | Positive Selection | WGD or Segmental |
CsaLecRLK4 | CsaLecRLK10 | 0.77 | 0.65 | 0.84 | 25.67 | Purifying Selection | WGD or Segmental |
CsaLecRLK12 | CsaLecRLK15 | 0.97 | 0.45 | 0.46 | 32.33 | Purifying Selection | WGD or Segmental |
CsaLecRLK17 | CsaLecRLK18 | 1.36 | 0.43 | 0.31 | 45.33 | Purifying Selection | WGD or Segmental |
CsaLecRLK19 | CsaLecRLK20 | 0.98 | 0.16 | 0.16 | 32.67 | Purifying Selection | WGD or Segmental |
CsaLecRLK22 | CsaLecRLK25 | 0.65 | 0.49 | 0.76 | 21.67 | Purifying Selection | WGD or Segmental |
CsaLecRLK27 | CsaLecRLK33 | 0.81 | 0.49 | 0.60 | 27.00 | Purifying Selection | WGD or Segmental |
CsaLecRLK35 | CsaLecRLK36 | 1.03 | 0.47 | 0.46 | 34.33 | Purifying Selection | WGD or Segmental |
CsaLecRLK8 | CsaLecRLK11 | 0.81 | 0.58 | 0.72 | 27.00 | Purifying Selection | Tandem |
CsaLecRLK13 | CsaLecRLK16 | 0.67 | 0.53 | 0.79 | 22.33 | Purifying Selection | Tandem |
CsaLecRLK21 | CsaLecRLK23 | 1.07 | 0.48 | 0.44 | 35.67 | Purifying Selection | Tandem |
CsaLecRLK24 | CsaLecRLK26 | 0.41 | 0.38 | 0.93 | 13.67 | Purifying Selection | Tandem |
CsaLecRLK28 | CsaLecRLK29 | 0.53 | 0.60 | 1.12 | 17.67 | Positive Selection | Tandem |
CsaLecRLK30 | CsaLecRLK31 | 0.48 | 0.14 | 0.29 | 16.00 | Purifying Selection | Tandem |
CsaLecRLK6 | CsaLecRLK7 | 0.96 | 0.57 | 0.59 | 32.00 | Purifying Selection | Dispersed |
CsaLecRLK5 | CsaLecRLK14 | 0.54 | 0.61 | 1.13 | 18.00 | Positive Selection | Proximal |
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Haider, M.S.; De Britto, S.; Nagaraj, G.; Gurulingaiah, B.; Shekhar, R.; Ito, S.-i.; Jogaiah, S. Genome-Wide Identification, Diversification, and Expression Analysis of Lectin Receptor-Like Kinase (LecRLK) Gene Family in Cucumber under Biotic Stress. Int. J. Mol. Sci. 2021, 22, 6585. https://doi.org/10.3390/ijms22126585
Haider MS, De Britto S, Nagaraj G, Gurulingaiah B, Shekhar R, Ito S-i, Jogaiah S. Genome-Wide Identification, Diversification, and Expression Analysis of Lectin Receptor-Like Kinase (LecRLK) Gene Family in Cucumber under Biotic Stress. International Journal of Molecular Sciences. 2021; 22(12):6585. https://doi.org/10.3390/ijms22126585
Chicago/Turabian StyleHaider, Muhammad Salman, Savitha De Britto, Geetha Nagaraj, Bhavya Gurulingaiah, Ravikant Shekhar, Shin-ichi Ito, and Sudisha Jogaiah. 2021. "Genome-Wide Identification, Diversification, and Expression Analysis of Lectin Receptor-Like Kinase (LecRLK) Gene Family in Cucumber under Biotic Stress" International Journal of Molecular Sciences 22, no. 12: 6585. https://doi.org/10.3390/ijms22126585