Unravelling the regulatory network and evolutionary aspects of the ARID gene family of Arabidopsis through in- silico analyses

Abstract The AT-rich interaction domain ( ARID ) gene family is a conserved group of DNA- binding proteins involved in chromatin remodeling, transcriptional regulation, and eukaryotic developmental processes. Despite having functional importance, no comprehensive genome-wide study has been conducted on this gene family. In this study, genome-wide analysis was conducted through an in-silico approach on the model plant Arabidopsis thaliana to characterize the ARID gene family. A total of ten AtARID genes were identified and systematically analyzed for their chromosomal localization, gene structure, gene ontology, conserved motifs, cis-regulatory elements, phylogenetic relationships, and expression profiles. The predicted AtARID proteins vary widely in molecular weight, isoelectric point, and exon–intron organization, indicating structural and functional diversification. All identified genes contained the ARID domain and were localized to chromosomes 1–4, with subcellular localization in the nucleus. Analysis revealed the presence of core cis-elements (TATA- and CAAT-box) and multiple hormone and stress-responsive motifs, including ABRE and W-box, implying complex transcriptional regulation. Phylogenetic and synteny analyses across Arabidopsis thaliana , rice, maize, wheat, citrus, and tomato revealed five major clades while several segmental duplication events were identified within Arabidopsis thaliana . Transcriptomic profiling showed tissue-specific expression patterns, with AtARID_07 and AtARID_09 predominantly expressed in reproductive tissue. Overall, this work provides a baseline framework for future functional investigations of AtARID genes in plant growth, stress responses, and metabolism, and will further facilitate exploration of this gene family in relation to plant reproduction.