Evolutionary Dynamics and Expression Divergence of the Gene Family During Recent Speciation of AA-Genome Species.

To investigate the evolutionary trajectory during the recent speciation of AA-genome species, we conducted a comprehensive analysis of the gene family across eight species. We identified 1093 genes in total and systematically examined their evolutionary history, gene family expansion, and expression divergence. Our results revealed that extensive lineage-specific expansions occurred in AA-genome species, which were primarily generated by proximal and tandem duplications, with a particularly notable episode in Type-I genes. Despite the significant expansion, Type-I genes were generally expressed at low levels or not expressed across various organs. In contrast, the expansion of Type-II genes was primarily observed in the AG, AGL12, SOC1, GGM13, and MIKC* subfamilies, which exhibited high levels of expression in reproductive organs such as panicles and stigmas. Additionally, we found species-specific gene expression in the two out-crossing wild rice species, and . Notably, a unique gene in exhibited high expression levels in rhizomes and stems, which may be associated with the species' distinctive rhizomatous growth habit.