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Genome-wide identification of the BURP domain-containing genes in Phaseolus vulgaris

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Abstract

Plant-specific BURP domain-containing proteins have an essential role in the plant's development and stress responses. Although BURP domain-containing proteins have been identified in several plant species, genome-wide analysis of the BURP gene family has not been investigated in the common bean. In the present study, we identified 11 BURP family members in the common bean (Phaseolus vulgaris) genome with a comprehensive in silico analysis. Pairwise alignment and phylogenetic analyses grouped PvBURP members into four subfamilies [RD-22 like (3), PG1β-like (4), BNM2-like (3), and USP-like (1)] according to their amino acid motifs, protein domains and intron–exon structure. The physical and biochemical characteristics of amino acids, motif and intron–exon structure, and cis-regulatory elements of BURPs members were determined. Promoter regions of BURP members included stress, light, and hormone response-related cis-elements. Therefore, expression profiles of PvBURP genes were identified with in silico tools and qRT-PCR analyses under stress (salt and drought) and hormone treatment (ABA, IAA) in the current study. While significant activity changes were not observed in BURP genes in RNA-seq data sets related to salt stress, it was determined that some BURP genes were expressed differently in those with drought stress. We identified 12 different miRNA, including miRNA395, miRNA156, miRNA169, miRNA171, miRNA319, and miRNA390, targeting the nine PvBURP genes using two different in silico tools based on perfect or near‐perfect complementarity to their targets. Here we present the first study to identify and characterize the BURP genes in common bean using whole-genome analysis, and the findings may serve as a reference for future functional research in common bean.

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Funding

This research was supported by Research Fund of Ondokuz Mayıs University PYO.ZRT.1901.17.010.

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Correspondence to Musa Kavas.

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Table S1. Primer sequences of PvBURP genes for qRT-PCR analysis (XLSX 11 kb)

Table S2. Location of the BURP domain and signal peptide in BURP proteins (XLSX 12 kb)

12298_2021_1052_MOESM3_ESM.xlsx

Table S3. A-biotic stress response-related cis-elements in the promoter sequences of PvBURPs covering the upstream region of 2000 nucleotides from the gene start codon (XLSX 11 kb)

Table S4. Secondary structures of PvBURP proteins (XLSX 25 kb)

Table S5. Expression profiles of PvBURP genes in different RNA-seq dataset based on log2FC value (XLSX 11 kb)

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Figure S1. Conserved motifs in PvBURP proteins were obtained through the MEME Suit. Conserved motifs were analyzed by choosing 15 motifs and repeating any number of motifs. (PNG 1192 kb)

Figure S2. 3D structure of PvBURP proteins illustrated using Phyre2 server with an “intensive” mode. (PNG 640 kb)

Figure S3. Prediction of transmembrane helices in PvBURP proteins. (PNG 534 kb)

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Kavas, M., Yıldırım, K., Seçgin, Z. et al. Genome-wide identification of the BURP domain-containing genes in Phaseolus vulgaris. Physiol Mol Biol Plants 27, 1885–1902 (2021). https://doi.org/10.1007/s12298-021-01052-9

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  • DOI: https://doi.org/10.1007/s12298-021-01052-9

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