Evolution of Plant AIG1-like Proteins: Different Modes of Sequence Divergence and Their Contributions to Functional Diversification

AIG1 (avrRpt2-induced gene 1)-like proteins are a class of GTPases that play crucial roles in plants, functioning both in chloroplast protein import and disease resistance. However, their evolutionary history and the mechanisms driving this functional diversification remain poorly understood. Here, we performed a comprehensive genomic and evolutionary analysis of this gene family across the plant kingdom. We identified 90 <i>AIG1</i>-like genes from 11 sequenced plant species, representing major lineages from green algae to angiosperms. Phylogenetic analysis revealed that plant AIG1-like proteins form three monophyletic lineages corresponding to the <i>Toc34</i>, <i>Toc159</i>, and <i>IAN</i> subfamilies, which originated via two ancient duplications predating the divergence of green algae and land plants. These lineages exhibit dramatically divergent evolutionary patterns. The <i>Toc34</i> subfamily is evolutionarily conserved, maintaining stable copy numbers and gene structure, indicative of strong functional constraints in its core role in plastid import. In contrast, the <i>Toc159</i> and <i>IAN</i> subfamilies have undergone dynamic expansion via lineage-specific duplication mechanisms, including segmental duplication and prolific tandem duplication, respectively. Notably, we uncovered a novel mechanism for generating head-to-head tandem duplicates in the <i>IAN</i> subfamily, mediated by recombination between inverted repeats. Our analysis of ancestral gene numbers and gene gain/loss dynamics further highlights that functional diversification was driven by both the acquisition of distinct C-terminal targeting domains (M and TM domains) and profound differences in evolutionary rates and duplication modes among subfamilies. This study provides the first full-scale evolutionary framework for plant <i>AIG1</i>-like genes, establishing that functional specialization is rooted in distinct modes of sequence and genomic evolution.