Comparative genomic and gene expression study of Dirigent genes in genus Dendrobium: a bioinformatics analysis

Dirigent (DIR) proteins guide lignan and lignin formation and play important roles in plant defense and stress responses. Although genome assemblies have been completed for several Dendrobium species, the functional characterization and expression patterns of DIR genes in this genus remain limited. In this study, comparative genomic and transcriptomic analyses of DIR genes were performed across 17 chromosome-level Dendrobium genomes. A total of 202 DIR genes were identified, with 9–16 genes per species. Phylogenetic analysis classified these genes into five subfamilies (DIR‑a, DIR‑b/d, DIR‑c, DIR‑e, and DIR‑g). DIR‑b/d is the most abundant subfamily and is present in all species, whereas DIR‑a, DIR‑c, and DIR‑e are restricted to certain species. The DIR genes are distributed across 12 orthogroups (OGDIR1–OGDIR12). OGDIR1 is present in all 17 species with copy numbers ranging from 1 to 6, while OGDIR12 is unique to D. aphyllum. Gene duplication analysis revealed that whole‑genome duplication, tandem duplication, transposed duplication, and dispersed duplication all contributed to the expansion of DIR genes. Ka/Ks analysis showed that OGDIR1–OGDIR9 are under purifying selection, whereas OGDIR10 is under positive selection. Synteny analysis identified 4–9 syntenic DIR gene pairs between species. Transcriptome profiling demonstrated that DIR genes are generally expressed at low levels in pseudobulbs but are significantly upregulated in roots and flower buds, with most upregulated genes belonging to the DIR‑b/d subfamily. The results reveal the genomic diversity, evolutionary dynamics, and organ‑specific expression patterns of DIR genes in Dendrobium. These findings provide a foundation for further functional studies of DIR genes and their potential applications in improving the quality of Dendrobium species. Dirigent (DIR) proteins guide lignan and lignin formation and play important roles in plant defense and stress responses. Although genome assemblies have been completed for several Dendrobium species, the functional characterization and expression pa... [2656 chars]