Near telomere-to-telomere (T2T) level genome assembly of the critically endangered plant Magnolia zenii (Magnoliaceae)

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.