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Comparative Genomic Analysis of GARP Transcription Factor Family in Legumes and Identification of Stress-Responsive Candidate Genes

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Abstract

The GARP transcription factors have been identified for multiple biological functions throughout the life cycle of a plant. Despite of its involvement in crucial functions, systematic study of GARPs remains obscure in plants. In this study, we explored the genomic, molecular, and evolutionary perspectives of the GARP gene family in the three major leguminous plants, namely chickpea (Cicer arietinum), soybean (Glycine max), and barrel clover (Medicago truncatula). Here, we identified 53, 56, and 107 GARP genes in Cicer, Medicago, and Glycine, respectively. They were classified into four clades and two sub-clades as per phylogenetic analysis, and the result was supported by consensus motifs, domain organization, and exon–intron structures. Detailed comparative analysis indicates conservation of the GARP gene family in plants. Identification of paralogous and orthologous gene pairs revealed that the expansion of this family occurs mainly through genome duplication in legumes. Additionally, the three-dimensional structure and functional enrichment analysis indicated their major role in signaling, growth, development, and stress processes. The chickpea GARP genes were also characterized for their transcript modulation in diverse plant organs and during pathogenic stress. Differential regulation of 24 CaGARP genes was observed during Ascochyta Blight (AB) stress. Characterization of AB-responsive genes reveals an over-representation of stress and hormone-binding elements on the promoter of CaGARPs. Additionally, interactome analysis also confirms the role of GARPs in plant stress and development. Our findings not only provide a handful of stress-responsive genes but also lay the foundation for prospective functional studies of GARPs in legumes.

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Acknowledgements

RS acknowledges University Grants Commission (UGC), India for the SRF fellowship. The authors declare that there is no conflict of interest.

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Authors and Affiliations

  1. National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India

    Ritu Singh, Ashutosh Pandey & Praveen Kumar Verma

  2. Plant Immunity Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India

    Praveen Kumar Verma

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  1. Ritu Singh
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  2. Ashutosh Pandey
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Contributions

Conception and design—RS and PKV, analysis and interpretation of the data—RS, drafting of the article—RS, critical revision of the article for important intellectual content—AP and PKV, final approval of the article—PKV, obtaining of funding—PKV.

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Correspondence to Praveen Kumar Verma.

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Supplementary Information

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344_2022_10746_MOESM1_ESM.tiff

Supplementary file1 Fig. S1. Multiple sequence alignment of GARP B-motif. (A) Cicer, (B) Medicago, and (C) Glycine. Amino acid sequences of GARP B-motif were aligned using the ClustalX2.1 (http://www.clustal.org) program and visualized through Jalview software (Waterhouse et al., 2009). The conserved GARP motif is boxed in blue color and the highlighted colored region indicates the conserved amino acid residues among the sequences (TIFF 15342 kb)

344_2022_10746_MOESM2_ESM.tiff

Supplementary file2 Fig. S2. The logo and sequences of the conserved motifs are identified in three legumes. (A) Cicer, (B) Medicago, and (C) Glycine. The motifs are predicted using MEME v5.4.1 (TIFF 16487 kb)

344_2022_10746_MOESM3_ESM.tiff

Supplementary file3 Fig. S3. Prediction of stress-responsive GARP genes. The phylogenetic tree of identified GARP genes is prepared by utilizing functionally characterized GARP members. Representation of the phylogenetic tree of (A) Cicer, (B) Medicago, and (C) Glycine. The tree was constructed using the neighbor-joining method in Mega7 (Kumar, Stecher, and Tamura, 2016). Bootstrap values are obtained from 1000 iterations and indicated by circles on each branch. The branches of different clades are marked in different colors (TIFF 11979 kb)

344_2022_10746_MOESM4_ESM.tiff

Supplementary file4 Fig. S4. Predicted promoter element for putative AB-stress-responsive CaGARPs. The 1500 bp promoter sequences are analyzed through PlantPan (Chang et al., 2008) and PlantCare databases (Lescot et al., 2002) database. The scale represents the position of promoter elements. The lines denote promoter sequences and identified elements are represented by different color boxes (TIFF 12868 kb)

344_2022_10746_MOESM5_ESM.tiff

Supplementary file5 Fig. S5. Representation of protein-protein interaction network. CaGARPs are mapped on Arabidopsis STRINGDB (https://string-db.org). The network is visualized through Cytoscape v3.6.2 (TIFF 4583 kb)

Supplementary file6 Table S1. Identified GARP genes in Cicer and their physicochemical properties (DOCX 32 kb)

Supplementary file7 Table S2. Identified GARP genes in Medicago and their physicochemical properties (DOCX 43 kb)

Supplementary file8 Table S3. Identified GARP genes in Glycine and their physicochemical properties (DOCX 68 kb)

344_2022_10746_MOESM9_ESM.docx

Supplementary file9 Table S4. The number of identified GARPs, the total number of annotated genes, and genome size of Cicer, Medicago, and Glycine (DOCX 13 kb)

Supplementary file10 Table S5. List of orthologous and paralogous GARP genes and their Ka/Ks ratio (XLSX 22 kb)

Supplementary file11 Table S6. Identified GO processes in Cicer, Medicago, and Glycine (XLSX 45 kb)

344_2022_10746_MOESM12_ESM.docx

Supplementary file12 Table S7. Fold change of the differentially expressed GARP genes during AB-stress in chickpea (DOCX 19 kb)

344_2022_10746_MOESM13_ESM.xlsx

Supplementary file13 Table S8. Identified promoter elements for putative AB-stress-responsive CaGARP genes (XLSX 140 kb)

344_2022_10746_MOESM14_ESM.xlsx

Supplementary file14 Table S9. Predicted transcription factor binding sites for putative AB-stress-responsive CaGARP genes (XLSX 348 kb)

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Singh, R., Pandey, A. & Verma, P.K. Comparative Genomic Analysis of GARP Transcription Factor Family in Legumes and Identification of Stress-Responsive Candidate Genes. J Plant Growth Regul 42, 6005–6020 (2023). https://doi.org/10.1007/s00344-022-10746-7

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