High-quality chromosome-level genome assembly of Davidia involucrata reveals evolutionary insights into tannin biosynthesis and bract development

The rare relic species Davidia involucrata is celebrated for its ornamental white bracts and high ellagitannin content. In this work, we report the chromosome-level genome assembly of D. involucrata, employing a hybrid sequencing approach combining Illumina, PacBio, and Hi-C platforms. The assembled genome spans 1101.83 Mb and contains 43,998 protein-coding genes. Phylogenetic analysis places D. involucrata within the Nyssaceae family, diverging from the Vitaceae lineage approximately 38.97 million years ago, with a lineage-specific WGD event post-divergence. Key gene families connected with tannin biosynthesis, such as CXE and DQD/SDH, were characterized. Tandem duplication clusters of these genes on chromosome 1 exhibit tissue-specific expression patterns and show collinearity with high-tannin species, highlighting their crucial roles in ellagitannin metabolism. Transcriptomic profiling of bracts and leaves provides molecular insights into bract whitening: upregulation of flavonoid biosynthesis genes (e.g., FLS and CHS) promotes flavonol accumulation, while the concomitant upregulation of chlorophyll degradation genes (e.g., SGR, PPH, and PAO) together with the downregulation of chlorophyll biosynthesis genes (e.g., HemA, HemF, and CRD) leads to the loss of green pigmentation. This high-quality genome assembly significantly advances our understanding of D. involucrata, offering valuable insights for its conservation and sustainable utilization while unraveling the evolutionary mechanisms driving tannin biosynthesis and floral development in relic plants.