Haplotype‐resolved genome assembly of Bletilla striata (Thunb.) Reichb.f. to elucidate medicinal value

SUMMARY Bletilla striata, commonly known as baiji, is a species used in traditional Chinese medicine; it is highly regarded for its medicinal applications and therefore has high economic value. Here, we report a high‐quality haplotype‐resolved genome of B. striata, haplotype A (2.37 Gb, with a scaffold N50 of 146.39 Mb and a contig N50 of 1.65 Mb) and haplotype B (2.43 Gb, with a scaffold N50 of 150.22 Mb and a contig N50 of 1.66 Mb), assembled from high‐fidelity (HiFi) reads and chromosome conformation capture (Hi‐C) reads. We find evidence that B. striata has undergone two whole‐genome duplication (WGD) events: an ancient WGD event shared by most monocots and a recent WGD event unique to all orchids. We also reconstructed the ancestral orchid karyotype (AOK) of 18 ancient chromosomes and the evolutionary trajectories of 16 modern B. striata chromosomes. Comparative genomic analysis suggests that the expanded gene families of B. striata might play important roles in secondary metabolite biosynthesis and environmental adaptation. By combining genomic and transcriptomic data, we identified the 10 core members from nine gene families that were probably involved in B. striata polysaccharide (BSP) biosynthesis. Based on virus‐induced gene silencing (VIGS) and yeast two‐hybrid experiments, we present an MYB transcription factor (TF), BsMYB2, that can regulate BSP biosynthesis by directly interacting with eight key BSP‐related genes: sacA1, HK1, scrK1, scrK2, GPI1, manA1, GMPP1 and UGP2_1. Our study will enhance the understanding of orchid evolution and accelerate the molecular‐assisted breeding of B. striata for improving traits of medicinal value. Significance Statement We first report a high‐quality haplotype‐resolved genome of B. striata, Haplotype‐A (2.37 Gb with a scaffold N50 of 146.39 Mb) and Haplotype‐B (2.43 Gb with a scaffold N50 of 150.22 Mb), and exhibit a MYB transcription factor (TF), BsMYB2, which can regulate BSPs biosynthesis by directly interacting with eight key BSPs‐related gene. This study will enhance the understanding of orchid evolution and accelerate molecular‐assisted breeding of B. striata for improving medicinal‐value traits.