High-quality telomere-to-telomere genome assembly of the critically endangered tree Magnolia longipedunculata

Magnolia longipedunculata is a critically endangered tree endemic to southern China, valued for its ornamental flowers but with only 11 known wild individuals. As a member of Magnoliaceae—one of the earliest-diverging angiosperm lineages—it provides an important genomic resource for conservation and investigating early angiosperm evolution. Here, we report a high-quality telomere-to-telomere (T2T) genome assembly of M. longipedunculata generated using PacBio HiFi, Hi-C, Illumina, and RNA-seq data. The 2.16 Gb assembly was anchored onto 19 pseudo-chromosomes, showing high contiguity (contig N50: 54.53 Mb; scaffold N50: 151.43 Mb) and completeness (BUSCO: 96.6%; LAI: 15.21; Merqury QV: 41.70). Repetitive sequences occupy 81.93% of the genome, dominated by long terminal repeat retrotransposons (LTRs, 38.88%). A total of 24,470 protein-coding genes and 29,936 transcripts were annotated, of which 95.93% (28,718 proteins) were functionally characterized. This reference-grade genome provides a critical resource for conservation genetics, genome evolution, and comparative genomics within Magnoliaceae and across basal angiosperms.