The golden bell flower genome provides insights into its evolutionary history and reveals the potential genomic bases of its ecological divergence from weeping forsythia

The golden bell flower (GBF), a beloved flower that blooms in early spring, faces a significant challenge in genetic research and breeding due to the lack of available genomic data. Here, a genome of GBF with a genome size of 735.31 Mb and tiny gaps of 3,782 N were assembled. Our results showed GBF underwent two round of whole genome doubling (WGD) events. The more recent WGD events, along with subsequent structural variations in GBF and weeping forsythia, might lead to the divergence of GBF and weeping forsythia. Analysis of enriched KEGG pathways and Gene Ontology categories of the expanded and contracted genes indicated an increase in the GBF abilities of faster growth and stronger cold and drought tolerance since the separation of the two species. Our results showed that the effective population size (Ne) of the GBF species has been decreasing, declining from 0.352 Mya to 0.018 Mya. However, the stronger cold tolerance of GBF likely helped to alleviate the reduction of Ne during the Pleistocene glacial periods. The expansion of peroxidase (POD) and l-gulonolactone oxidase (GULO) genes and more POD and GULO genes with anaerobic and ABA-induced cis elements in GBF genome might be responsible for the strong waterlogging tolerance of GBF. Our study characterized the evolutionary history of GBF and the genomic bases for the ecological divergenece between GBF and weeping forsythia. Our genome provides genetic resources for future genetic and breeding studies on GBF and its related species.