Rosaceae phylogenomic studies provide insights into the evolution of new genes

Rosa banksiae, known as Lady Banks' rose, is a perennial ornamental crop and a versatile herb in traditional Chinese medicine. Given the lack of genomic resources, we assembled a HiFi and Nanopore sequencing-derived 458.58 Mb gap-free telomere-to-telomere high-quality R. banksiae genome with a scaffold N50 = 63.90 Mb. The genome of R. banksiae exhibited no lineage-specific whole-genome duplication compared with other Rosaceae. The phylogenomic analysis of 13 Rosaceae and Arabidopsis through a comparative genomics study showed that numerous gene families were lineage-specific both before and after the diversification of Rosaceae. Some of these genes are candidates for new genes that have evolved from parental genes through fusion events. Fusion genes are divided into three types: Type-I and Type-II genes contain two parental genes that are generated by duplication, distributed in the same and different regions of the genome, respectively; and Type-III can only be detected in one parental gene. Here, Type-I genes are found to have more relaxed selection pressure and lower Ks values than Type-II, indicating that these newly evolved Type-I genes may play important roles in driving phenotypic evolution. Functional analysis exhibited that newly formed fusion genes can regulate the phenotype traits of plant growth and development, suggesting the functional significance of these genes. This study identifies new fusion genes that could be responsible for phenotype evolution and provides information on the evolutionary history of recently diverged species in the Rosa genus. Our data represents the major progress in understanding the new fusion genes evolution pattern of Rosaceae and provides an invaluable resource for phylogenomic studies in plants.