Genome-wide identification, comprehensive characterization of transcription factors, cis-regulatory elements, protein homology, and protein interaction network of DREB gene family in Solanum lycopersicum

Abstract

Tomato is a drought-sensitive crop which has high susceptibility to adverse climatic changes. Dehydration-responsive element-binding (DREB) are significant plant transcription factors that have a vital role in regulating plant abiotic stress tolerance by networking with DRE/CRT cis-regulatory elements in response to stresses. In this study, bioinformatics analysis was performed to conduct the genome-wide identification and characterization of DREB genes and promoter elements in Solanum lycopersicum. In genome-wide coverage, 58 SlDREB genes were discovered on 12 chromosomes that justified the criteria of the presence of AP2 domain as conserved motifs. Intron–exon organization and motif analysis showed consistency with phylogenetic analysis and confirmed the absence of the A3 class, thus dividing the SlDREB genes into five categories. Gene expansion was observed through tandem duplication and segmental duplication gene events in SlDREB genes. Ka/Ks values were calculated in ortholog pairs that indicated divergence time and occurrence of purification selection during the evolutionary period. Synteny analysis demonstrated that 32 out of 58 and 47 out of 58 SlDREB genes were orthologs to Arabidopsis and Solanum tuberosum, respectively. Subcellular localization predicted that SlDREB genes were present in the nucleus and performed primary functions in DNA binding to regulate the transcriptional processes according to gene ontology. Cis-acting regulatory element analysis revealed the presence of 103 motifs in 2.5-kbp upstream promoter sequences of 58 SlDREB genes. Five representative SlDREB proteins were selected from the resultant DREB subgroups for 3D protein modeling through the Phyre2 server. All models confirmed about 90% residues in the favorable region through Ramachandran plot analysis. Moreover, active catalytic sites and occurrence in disorder regions indicated the structural and functional flexibility of SlDREB proteins. Protein association networks through STRING software suggested the potential interactors that belong to different gene families and are involved in regulating similar functional and biological processes. Transcriptome data analysis has revealed that the SlDREB gene family is engaged in defense response against drought and heat stress conditions in tomato. Overall, this comprehensive research reveals the identification and characterization of SlDREB genes that provide potential knowledge for improving abiotic stress tolerance in tomato.

Shade responses and resistant mechanisms in Spatholobus suberectus

“…With reference to literatures describing CRE [ [18] , [19] , [20] ], the phytohormone-, stress-, and development-related CREs in 18 flavonoid biosynthetic pathway genes promoter regions were identified in S. suberectus and visualized by heatmap ( Fig. 8 ).…”

Genome-Wide Identification of BTB Domain-Containing Gene Family in Grapevine (Vitis vinifera L.)

“…Several hormone-responsive cis-elements were also present in the promoters of VvBTB genes. For example, the As-I element involved in auxin and methyl jasmonate (MeJA) signaling was present in the promoters of several VvBTB genes [64]. Methyl jasmonate (MeJA) plays a crucial role in plant biotic stress resistance.…”

Transcriptomic Profiling of Tomato Leaves Identifies Novel Transcription Factors Responding to Dehydration Stress

“…Moreover, we compared the expression levels of six drought-responsive marker genes: SlDREB1 (Solyc06g050520), SlDREB2 (Solyc12g008350), SlDREB3 (Solyc04g072900), SlGRAS4 (Solyc01g100200), SlNCED (Solyc07g056570), and SlGA2OX7 (Solyc02g080120), which were previously reported to positively respond to drought stress [51][52][53][54]. Our results showed that these genes were upregulated by dehydration treatment, suggesting the identification of overlapping regulators of drought and dehydration response by transcriptomic profiling in this study (Figure S4).…”