Divergent evolution of genes in the genus : impacts of annuals and perennials' life history strategies.

Within the family , the genus is composed of two subgenera annuals (2n=40) and perennials. This life strategy transition may have differentially affected the evolution of various gene families. Its cultivated species has high level of susceptibility to major pathogens including viruses, bacteria and fungi. Understanding nucleotide-binding domain leucine-rich repeat () genes evolution in soybean is of paramount importance due to their central role in plant immunity and their potential in improving disease resistance in soybean cultivars. In this study, we investigated the significance of this annual-perennial transition on the macroevolution of genes in the genus . Our results reveal a remarkable distinction between annual species such as and , which exhibit an expanded ome compared to perennial species ( and ). Our evolutionary timescale analysis pinpoints recent accelerated gene duplication events for this expansion, which occurred between 0.1 and 0.5 million years ago, driven predominantly by lineage-specific and terminal duplications. In contrast, perennials initially experienced significant contraction during the diploidisation phase following the -specific whole-genome duplication event (~10 million years ago). Despite the reduction in the ome, perennial lineages exhibit a unique and highly diversified repertoire of genes with limited interspecies synteny. The investigation of gene gain and loss ratios revealed that this diversification resulted from the birth of novel genes following individual speciation events. Among perennials, , a well-known resistance resource, has the highest ratio of these novel genes in the tertiary gene pool. Our study suggests evolutionary mechanisms, including recombination and transposition, as potential drivers for the emergence of these novel genes. This study also provides evidence for the unbalanced expansion of the ome in the D subgenome compared with the A subgenome in the young allopolyploid . To the best of our knowledge, this is the first study to investigate the effect of annuality and perenniality life transition on the evolution of genes in the genus to identify its genomics resources for improving the resistance of soybean crop with global importance on the economy and food security.