Abstract
Berchemiella wilsonii (Schneid.) Nakai is one of the National Key Protected Wild Plants in China, and one of the 120 Plant Species with Extremely Small Populations in China. By combining PacBio HiFi sequencing, DNBSEQ sequencing and Hi-C sequencing, we have assembled a chromosome-scale, haplotype-resolved genome for B. wilsonii. The final assembled haplotype A and haplotype B genomes were 216.84 Mb and 217.69 Mb, anchored to 2n = 24 chromosomes, all chromosomal ends contain telomeric characteristic motifs (TTTAGGG), only haplotype A has one gap, both close to a T2T genome assembly, with contig N50 lengths of 18.24 Mb and 18.03 Mb, respectively. Further, BUSCO analysis showed an extremely high assembly completeness (98.9% complete BUSCO genes). The genome contains a total of 22,828 coding genes, of which 21,992 (96.34%) were functionally annotated. This is the first report of the genome of B. wilsonii and the high-quality genome will provide new insights into evolutionary history and taxonomic classification challenges of endangered plant species.