A chromosome-scale assembly and comparative genomics of the Yunnanopilia longistaminata

Yunnanopilia longistaminata is a rare forest vegetable, distributed in Yunnan and Guangxi Provinces of southeastern China. It is characterized by a unique flavor and rich nutritional value, making it a potential resource for dietary and medicinal applications. However, the absence of a high quality reference genome has limited the comprehensive development and utilization of this valuable plant resource. In this study, we present the chromosome-level genome assembly of Y. longistaminata using Nanopore sequencing and Hi-C technology. Its genome size was approximately 871.46 Mb, with a contig N50 of 8.47 Mb. A total of 870.61 Mb (99.97%) of the assembled sequences were anchored to ten chromosomes with a complete BUSCO score of 95.66%. Genome annotation revealed 22,050 protein-coding genes and 677.72 Mb of repetitive sequences. Phylogenomic analysis revealed Y. longistaminata forms a distinct clade with Santalum, exhibiting 1,525 expanded and 4,962 contracted gene families, and underwent two paleopolyploidization events. This frst high-quality Y. longistaminata genome will serve as a fundamental basis for future studies on functional genomics and genome evolution.