Abstract: Phoebe zhennan, an endemic species of Lauraceae in China, is an ecologically and economically important timber tree that has undergone severe population decline and is considered endangered. Despite its importance and threatened status, the absence of haplotype‐resolved genomic resources has hindered detailed genetic and evolutionary studies. Here, we report the first haplotype‐resolved chromosome‐level genome of P. zhennan using ONT ultra‐long reads and Hi‐C technology. The assemblies for Haplotype A (HapA, 956.20 Mb) and Haplotype B (HapB, 910.89 Mb) were each anchored to 12 chromosomes, with scaffold N50 values of 86.27 Mb and 77.12 Mb, respectively. A total of 33 757 and 33 651 protein‐coding genes were identified for HapA and HapB, respectively, of which 95% were functionally annotated. Comparative analyses revealed extensive structural heterozygosity, including 112 inversions, 2371 translocations, 6 059 780 single‐nucleotide polymorphisms (SNPs), 345 228 insertions, and 348 584 deletions. This haplotype‐resolved assembly further elucidates the characteristics of chromosomal structural variation and provides an important genetic resource for future studies on the evolution, conservation, and functional biology of P. zhennan.

Key words: chromosome‐level assembly, conservation genomics, haplotype‐resolved genome, Lauraceae, Nanmu, Phoebe zhennan