Abstract
Aquaporins (AQPs) are integral membrane channel proteins that facilitate water transport and contribute significantly to plant adaptation under drought stress. However, the evolutionary origins and mechanisms of functional diversity of this gene family remain to be elucidated. A comprehensive genome-wide analysis was therefore performed on 104 representative species spanning the green plant lineage, from algae to angiosperms. This study used two datasets: Taxon I (algae to eudicots) and Taxon II (angiosperms including drought-tolerant and drought-sensitive plants). By systematically optimizing the gene structure, codon preferences, motifs, and cis-elements of these two datasets, the molecular mechanisms of AQP genes in plant adaptation evolution and drought-tolerance evolution were revealed. The results of phylogenetic analysis indicate that the AQP gene family is divided into five main subfamilies: PIPs, NIPs, TIPs, SIPs, and XIPs. Through in-depth analysis of the evolution characteristics of each subfamily, it was found that the emergence and loss of different subclusters are related to the ecological adaptation needs of specific species. By systematically analyzing the evolutionary history of the members of PIPs and TIPs subfamilies and subclusters, and combining their gene expression patterns, it was confirmed that PIP2, TIP1, and TIP4 subcluster members exhibit more significant expression response characteristics under drought stress. This study is the first to analyze the evolutionary patterns and drought-tolerance mechanisms of the AQP gene family at a multidimensional scale, providing important molecular targets for crop drought resistance breeding.