Genome-wide comprehensive analysis the molecular phylogenetic evolution, functional divergence and tissue-specific expression of GH3 gene family in Salvia miltiorrhiza, Arabidopsis thaliana, and Oryza sativa

Auxin, as a central phytohormone and signaling molecule, plays a crucial role in plant growth and development. The activity of auxin is tightly regulated by the auxin-responsive <i>GH3</i> gene family. In this study, a total of 40 <i>GH3</i> genes in <i>A. thaliana</i>, <i>S. miltiorrhiza</i>, and <i>O. sativa</i> were identified and subjected to comprehensive study. Phylogenetic analysis revealed that those <i>GH3</i> genes can be classified into three distinct subgroups, with 11 pairs of paralogs identified. Genetic divergence analysis indicated that the <i>GH3</i> gene family had predominantly experienced purifying selection as evidenced by the Ka/Ks ratio being less than 1 for all 11 paralogs pairs. Positive selection analysis with the site and branch-site models further suggested that <i>SmGH3 AtGH3</i> and <i>OsGH3</i> genes had gone through purifying selective pressure for adaptive evolution. Motif analysis indicated that group-specific motifs may contribute to functional divergence across species and subgroups. Functional divergence analysis confirmed that subgroup-specific genes have experienced functional divergence during evolution, and elucidated the molecular mechanisms underlying their divergent functions. The tissue-specific expression analysis of <i>SmGH3 AtGH3</i> and <i>OsGH3</i> genes revealed that these genes might perform distinct functions in different tissues. This study performed a comprehensive bioinformatics analysis of the <i>GH3</i> gene family, offering valuable information to further elucidate the functional roles of <i>GH3</i> genes.