The haplotype-resolved, chromosome-scale genome assembly of the hexaploid Magnolia wufengensis provides valuable insights into genome evolution and the biosynthesis genes for flower color and fragrance

Magnolia wufengensis is a newly discovered species within the Magnoliaceae family. This tree is notable for its attractive fragrance and striking red flowers. Although M. wufengensis has significant ecological and ornamental value, a lack of genomic resources hindered use and protection of this tree. Here, a high-quality, haplotype-resolved chromosome-scale genome assembly of 11.98 Gb was generated, comprising 114 pseudochromosomes. Genome duplication analysis indicated that the hexaploid formation occurred approximately 6.8 million years ago (MYA), which is later than the divergence time from its sister species, M. sieboldii . Gene family analysis shows that species-specific and expanded genes in M. wufengensis enhance its ultraviolet tolerance, chromosome maintenance, and cell regeneration. Integrating gene expression assays identified four possible anthocyanin-related chemical compounds as the key determinants of color flower. The gene Mwu49047 , which encodes an anthocyanin UDP-glycosyltransferase, was predicted to be involved in the biosynthesis of these compounds. Enzyme assays revealed that Mwu49047 exhibits both cyanidin and delphinidin promiscuity and regiospecific catalytic activity toward the 3-OH position. Additionally, combining gene expression with metabolite assays in different tissues indicated that cis-Farnesene, (E)-2-octenal, and nonanal are the major components of the floral fragrance. Genes within one co-expression module were identified as regulators of the two aldehydes. This study provides a valuable genomic resource for M. wufengensis and novel insights into the regulation of its key economic traits.