A high-quality chromosome-level genome assembly of the endangered species Magnolia amoena

Magnolia amoena (Magnoliaceae), a deciduous tree endemic to eastern China, is valued for its striking floral diversity and traditional medicinal uses, yet remains understudied. To support its conservation and evolutionary research, we generated a high-quality chromosome-scale assembly using DNBSEQ-T7, PacBio HiFi, and Hi-C data. The final assembly spanned 1.87 Gb with a contig N50 of 36.92 Mb, of which 95.73% (1.79 Gb) was anchored onto 19 pseudochromosomes. Repetitive elements occupied 79.55% of the genome, dominated by long terminal repeats (57.72%) and DNA transposons (14.25%). A total of 39,739 protein-coding genes (mean length: 10.21 kb) were predicted, with 86.34% functionally annotated, alongside 270 miRNAs, 631 tRNAs, 668 rRNAs, and 4,133 snRNAs. Comparative genomic analysis across 11 magnoliid species identified 23,244 gene families in M. amoena, of which 1,905 were unique. Phylogenomic reconstruction strongly supported M. amoena as sister to M. biondii, with an estimated divergence time of ~18.5 Mya. Overall, this genome assembly lays a robust foundation for future research into the evolution, adaptation, and conservation of M. amoena.