The AT-hook motif nuclear localized (AHL) gene family encodes transcription factors pivotal in regulating plant growth, development, and responses to abiotic stimuli, including low temperature, salinity, darkness, and drought. In this study, we systematically identified 21 BpAHL genes in birch and characterized their sequence features, evolutionary relationships, and expression dynamics. Phylogenetic analysis classified BpAHLs into two clades (Clade-A and Clade-B) and three types (Type-I, -II, and -III), based on PPC domain and AT-hook motifs. Chromosomal mapping revealed an even distribution across nine chromosomes and one contig, with dispersed duplication events recognized as the major driver of BpAHL family expansion. Tissue-specific expression profiling uncovered striking divergence: Type-I BpAHLs displayed root-predominant expression, whereas Type-II/III BpAHLs were highly expressed in plant flowers and leaves. Notably, Type-II/III BpAHL genes in leaves showed distinct expression patterns in response to cold and heat stresses, while Type-I BpAHLs in roots were down-regulated under salt stress. This study provides a comprehensive phylogenomic and functional analysis of the AHLs in birch, providing insights into their roles in enhancing abiotic stress resilience in forest trees.

Background: Su(var)3-9 SET genes encode key histone methyltransferases that catalyze H3K9 methylation, a modification generally associated with heterochromatin formation and transcriptional repression. Methods: We identified 23 GmSu(var)3-9 SETs and systematically characterized their tissue-specific epigenetic modifications as well as their phylogenetic relationships, chromosomal distributions, conserved domains, gene structures, GO annotations, collinearity, cis-regulatory elements, and expression profiles across diverse tissues and under salt stress. Results: These genes were divided into seven groups, exhibiting diverse structures and uneven distribution on chromosomes. Gene structure and conserved motif analyses revealed high structural diversity among family members, with variations in intron–exon distribution, conserved motifs, and functional domains. Promoter analysis detected multiple cis elements responsive to light, hormones, and abiotic stresses. Most genes showed preferential expression in meristems, roots, and leaves, and responded to salt stress. Co-expression network analysis revealed that these genes were co-expressed with stress- and development-related genes. GmSUVH12 histone modifications exhibited obvious tissue specificity. Conclusions: Overall, these results provided insights into the evolutionary and functional roles of GmSu(var)3-9 SETs in soybean.