Abstract
TCP proteins are plant-specific transcription factors that have multipurpose roles in plant developmental procedures and stress responses. Therefore, a genome-wide analysis was performed to categorize the TCP genes in the rapeseed genome. In this study, a total of 80 BnTCP genes were identified in the rapeseed genome and grouped into two main classes (PCF and CYC/TB1) according to phylogenetic analysis. The universal evolutionary analysis uncovered that BnTCP genes had experienced segmental duplications and positive selection pressure. Gene structure and conserved motif examination presented that Class I and Class II have diverse intron-exon patterns and motifs numbers. Overall, nine conserved motifs were identified and varied from 2 to 7 in all TCP genes; and some of them were gene-specific. Mainly, Class II (PCF and CYC/TB1) possessed diverse structures compared to Class I. We identified four hormone- and four stress-related responsive cis-elements in the promoter regions. Moreover, 32 bna-miRNAs from 14 families were found to be targeting 21 BnTCPs genes. Gene ontology enrichment analysis presented that the BnTCP genes were primarily related to RNA/DNA binding, metabolic processes, transcriptional regulatory activities, etc. Transcriptome-based tissue-specific expression analysis showed that only a few genes (mainly BnTCP9, BnTCP22, BnTCP25, BnTCP48, BnTCP52, BnTCP60, BnTCP66, and BnTCP74) presented higher expression in root, stem, leaf, flower, seeds, and silique among all tested tissues. Likewise, qRT-PCR-based expression analysis exhibited that BnTCP36, BnTCP39, BnTCP53, BnTCP59, and BnTCP60 showed higher expression at certain time points under various hormones and abiotic stress conditions but not by drought and MeJA. Our results opened the new groundwork for future understanding of the intricate mechanisms of BnTCP in various developmental processes and abiotic stress signaling pathways in rapeseed.
Highlights
Transcription factors (TFs) contribute to plant growth and development, regulate gene expression, and play a significant role in several cellular/biological processes (Hoang et al, 2017; Karaaslan et al, 2020)
A sum of 80 BnTCP genes was identified with the TCP domain (Table 1)
Gene length varied from 531 bp (BnTCP10) to 9,673 bp (BnTCP40), the CDS length varied from 531 bp (BnTCP10) to 5,193 bp (BnTCP40), and the amino acid length varied from 176 (BnTCP10) to 1,730 (BnTCP40) amino acids
Summary
Transcription factors (TFs) contribute to plant growth and development, regulate gene expression, and play a significant role in several cellular/biological processes (Hoang et al, 2017; Karaaslan et al, 2020). The Teosinte Branched 1, Cycloidea, and Proliferating Cell Factors (TCP) gene family is a group of plantspecific TFs limited to higher plants (Cubas et al, 1999) These TFs have numerous roles in controlling plant growth and developmental procedures by directing cell proliferation (Cubas et al, 1999; Martín-Trillo and Cubas, 2010). These TFs are categorized by an extremely conserved 59-aminoacid basic helix–loop–helix (bHLH) motif at the N-terminus nominated as the TCP domain (Aggarwal et al, 2010). This supposed R domain was anticipated to develop a hydrophilic-helix or α-coiled-coil structure that facilitates the protein-protein interactions in plants (Cubas et al, 1999)
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