Functional divergence and adaptive selection of KNOX gene family in plants

KNOTTED-like homeodomain ( ) genes are transcriptional regulators that play an important role in morphogenesis. In the present study, a comparative analysis was performed to investigate the molecular evolution of the characteristics of the gene family in 10 different plant species. We identified 129 gene family members, which were categorized into two subfamilies based on multiple sequence alignment and phylogenetic tree reconstruction. Several segmental duplication pairs were found, indicating that different species share a common expansion model. Functional divergence analysis identified the 15 and 52 amino acid sites with significant changes in evolutionary rates and amino acid physicochemical properties as functional divergence sites. Additional selection analysis showed that 14 amino acid sites underwent positive selection during evolution, and two groups of co-evolutionary amino acid sites were identified by Coevolution Analysis using Protein Sequences software. These sites could play critical roles in the molecular evolution of the gene family in these species. In addition, the expression profiles of duplicated genes demonstrated functional divergence. Taken together, these results provide novel insights into the structural and functional evolution of the gene family.