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Integrated bioinformatics analyses identified SCL3-induced regulatory network in Arabidopsis thaliana roots

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Abstract

Objectives

To uncover key genes and pathways regulated by SCL3, a GRAS transcription factor, in the context of gibberellin (GA) in the roots of the model plant Arabidopsis thaliana.

Results

Gene expression profiles of ga1-3 mutant and ga1-3 and scl3 double mutant are considerably similar to each other, revealed by Principal Component Analysis (PCA). More than 400 significantly Differentially Expressed Genes (DEGs) among the Arabidopsis thaliana roots of ga1-3 mutant, ga1-3 and scl3 double mutant and GA loss/SCL3 gain mutant were uncovered by comprehensive bioinformatics analyses. Protein synthesis pathway, including RPL proteins, RPS proteins, etc., and flavonoid biosynthesis pathway, including TT4, F3H, TT5, CHIL, etc. were significantly increased when SCL3 expression was higher than normal by means of pathway enrichment analysis and protein–protein interaction analysis, which is further supported by comparison analyses between wild type samples and SCL3 overexpressed roots.

Conclusion

Protein synthesis and flavonoid biosynthesis were regulated by SCL3 in the context of GA in Arabidopsis thaliana root system identified by comprehensive bioinformatic analyses.

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Acknowledgements

The authors gratefully acknowledge the financial support of Zhejiang Provincial Natural Science Foundation (No. LQ18C010005).

Supporting information

Supplementary Table 1 DEGs analyzed by CytoHubba to determine key genes responsible for the gene expression cascade alteration. 12 algorithms were utilized for identification of the most reliable hub genes, and 46 hub gens were selected totally.

Supplementary Figure 1 Data quality evaluation of GSE61104 samples

Supplementary Figure 2 Volcano plot of differential genes between ga and ga/scl3

Supplementary Figure 3 Heatmap of the top 1000 differentially expressed genes between ga, ga/scl3 and ga/SCL3OE

Supplementary Figure 4 Interrelation analysis between differential pathways between Col and SCL3OE

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Correspondence to Zhi-Qiang Liu.

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Weng, CY., Zhu, MH., Liu, ZQ. et al. Integrated bioinformatics analyses identified SCL3-induced regulatory network in Arabidopsis thaliana roots. Biotechnol Lett 42, 1019–1033 (2020). https://doi.org/10.1007/s10529-020-02850-z

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