Genome-wide identification and analysis of the AT-hook motif nuclear localized (AHL) gene family in Citrus sinensis: expression profiles during fruit maturation and in response to pathogen stress

Citrus plants are widely grown in tropical and subtropical areas worldwide and are among the most important fruit crops in the world. AHL proteins, belonging to a family of transcription factor, play important roles in plant growth and development as well as response to various stresses through protein-DNA and protein-protein interactions. The gene families encoding AHLs have been identified in the Citrus sinensis genome, and comprehensive analyses have been performed on their physical and chemical properties, subcellular localization, cis-regulatory elements, conserved motifs, and tertiary structures. Furthermore, we examined their expression patterns during fruit development and in response to biotic stress using RNA-seq data. Our findings identified a total of 20 CsAHL genes, which are unevenly distributed across seven chromosomes. Phylogenetic analysis indicated that CsAHLs are organized into two clades, A and B, which are further subdivided into three types: I, II, and III. Collinearity analysis revealed six duplication events among the 20 CsAHLs. Temporal and spatial expression profiling indicate that CsAHL2, CsAHL4, CsAHL5, and CsAHL8 are likely involved in the process of fruit development. Furthermore, expression patterns observed under biotic stress conditions suggest a higher FPKM values at three time points compared to prior point. Subcellular localization studies have demonstrated that all above five proteins are situated within the cell nucleus. This study offers a foundational theoretical framework for elucidating the biological functions of CsAHLs.