Genome-Wide Characterization and Multidimensional Transcriptome Profiling of the SABATH Methyltransferase Gene Family in Sunflower (Helianthus annuus L.)

Plant SABATH methyltransferases contribute to volatile formation, hormone homeostasis and stress responses, but their family-wide organization in sunflower remains poorly characterized. Using the HanXRQr2.0-SUNRISE reference genome, we identified 33 high-confidence HaSABATH genes and integrated phylogenetic, duplication, synteny, promoter and protein-structure analyses with expression profiles from 200 public RNA sequencing (RNA-seq) libraries representing 87 distinct conditions. Twelve genes belonged to the salicylic acid/jasmonic acid methyltransferase-related Clade I, 19 to the benzoic acid/salicylic acid methyltransferase-related Clade II, and two to other lineages. Tandem, proximal, dispersed and whole-genome/segmental duplication contributed to the family, with overlapping tandem and segmental evidence for HaSABATH4 and HaSABATH15. Eleven reliable nonsynonymous-to-synonymous substitution ratios were below one. Most predicted proteins showed high model confidence. Across the sampled conditions, Clade I members generally showed higher expression levels and broader expression, while many Clade II members were weakly expressed or condition-biased. HaSABATH4 and HaSABATH6 were prioritized for follow-up under combined saline–alkali stress. This integrated analysis links evolutionary context to expression divergence and provides candidates for targeted biochemical and genetic studies.