Chromosome-level genome assembly provides insights into flavonoid biosynthesis in stems and leaves and fatty acid biosynthesis in kernels of Erythropalum scandens.

BACKGROUND

Erythropalum scandens, a perennial woody vine, is acknowledged for its substantial medicinal and edible applications. A high-quality genome for E. scandens was constructed employing PacBio + Hi-C + Illumina sequencing technologies.

RESULTS

The resultant genome assembly reached an approximate size of 2.03 Gb, featuring a contig N50 of 4.09 Mb, with 11 pseudochromosomes successfully established. Gene structural annotation identified 89.39% of repetitive sequences and 23,346 high-quality protein-coding genes within the assembled genome. Comparative genomic analysis revealed that E. scandens shares the closest evolutionary relationship with Santalum album and Malania oleifera, with two whole-genome duplication events estimated to have occurred approximately 18 and 120 million years ago. Through transcriptomic and metabolomic analyses of stems, leaves, and kernels, 34 genes and 12 enzymes were identified as key contributors to flavonoid biosynthesis predominantly in stems and leaves, whereas 30 genes and 14 enzymes were primarily implicated in the formation of oil bodies in plastids and the endoplasmic reticulum from fatty acid biosynthesis.

CONCLUSION

This investigation provides a genomic framework for E. scandens, elucidates the biosynthetic mechanisms of flavonoids in stems and leaves and fatty acids in kernels, and offers a theoretical foundation for advancing its medicinal and edible potential.