A haplotype-resolved genome assembly of Anoectochilus roxburghii

Anoectochilus roxburghii, a highly valued medicinal plant in traditional Chinese medicine, exhibits unique pharmacological properties and broad application value. In this study, we de novo assembled and annotated haplotype-resolved chromosome-level genomes of A. roxburghii cultivar 'Xiaoyuanye' by integrating PacBio HiFi reads and Hi-C data. The final assembly sizes were 1.92 Gb and 1.93 Gb, with contig N50 values of 22.72 Mb and 22.17 Mb, respectively. A total of 26,239 and 26,324 protein-coding genes were annotated, establishing a high-quality genomic resource for further research. Moreover, comparative genomic analysis revealed that A. roxburghii possesses 1,060 unique gene families and has undergone significant expansion of 2,100 gene families during evolution, providing crucial theoretical insights into the adaptive evolution of Orchidaceae species. The availability of the high-quality genomic data providing a crucial genetic foundation for elucidating the biosynthetic mechanisms and regulatory networks of pharmacologically active compounds in A. roxburghii.