Pan-genomic insights into RLK family evolution and adaptation in Dioscorea alata

Dioscorea alata (greater yam) is a vital tuber crop underpinning global food security, while this crop suffers great reduction due to diseases like anthracnose, yam mosaic virus, and tuber rot. Receptor-like kinases (RLKs) play pivotal role in plant disease resistance, transducing plant immune signal. Yet the evolutionary dynamics of RLKs remain underexplored in D. alata . Here, we leveraged seven chromosome-level D. alata genomes to characterize the pan-RLKome of D. alata , identifying 4,119 RLK genes across 48 subfamilies. Our analysis revealed moderate variation in total RLK numbers but striking subfamily-specific expansions on several chromosome hotspots driven primarily by whole-genome/segmental duplication. Phylogenomic reconstruction uncovered pervasive extracellular domain swaps, fusions, and losses, contributing to diversified RLK architectures. Selection pressure analyses showed that purifying selection has maintained core RLK functions, while positive selection drove adaptive evolution in stress-associated subfamilies. Our study uncovers the pan-genomic basis of RLK evolution in D. alata , highlighting how duplication mechanisms and domain plasticity underpin functional innovation and environmental adaptation in this vital crop.