Abstract
Magnolia zenii (Magnoliaceae) is an extremely endangered tree species endemic to eastern China, has only 115 individuals remaining in the wild. By integrating PacBio HiFi (49×), Oxford Nanopore (ONT; 101×) long-read sequencing, and Hi-C chromatin interaction data, we achieved a high-quality chromosome-level genome with scaffold N50 of 86 Mb, covering 99.97% of the estimated genome size. The genome annotation predicted 74,782 protein-coding genes and revealed a repetitive sequence content of 72.87%, dominated by long terminal repeat (LTR) retrotransposons (53.59%). The mitochondrial (915,126 bp) and chloroplast (160,079 bp) genomes were fully characterized. BUSCO analysis confirmed 99.4% genome completeness and 98.4% gene annotation completeness. This genomic resource provides a foundation for studying the genetic mechanisms underlying its endangered status and future horticultural.