The chromosome-scale genome provides clues to understanding the sex variation of a willow plant Salix variegata Franch

Salix variegata is a widely distributed species in the genus Salix, with high medicinal, economic, ecological restoration, and ornamental value. In this study, we assemble a 386.53 Mb and Contig N50 length of 13.66 Mb chromosomal-scale genome of S. variegata using PacBio ccs and Hi-C sequencing. Like other plants in the genus Salix, S. variegata has undergone two whole genome duplication (WGD), and the most recent WGD and LTR insertion may affect the genome size. Based on the assembled high-quality genome, we further combined cytology, transcriptomics, and metabolomics to explore the gene regulatory networks and their metabolite dynamics during different periods of female (F), male (M), and hybrid inflorescences (H). The results of cytological dynamics showed that female and male flowers in H did not differ from those in F and M, respectively, while transcriptional and metabolic analyses indicated differences in some phytohormones (ethylene, abscisic acid, jasmonic acid, and gibberellin) and sugar components. These metabolites and their regulated genes (17 key genes) and transcription factors (MYC2, PIF4, DELLA, CTR1) may be related to the sex variation of S. variegata. Our results provide a more comprehensive genome resource but also deepen the overall understanding of sex variation in the species. The study of sex variation in this class of dioecious plants can help us better understand the importance of genetic diversity and its role in evolution.