A chromosome-level genome assembly of Cistanche deserticola provides insights into its evolution and molecular mechanisms of parasitism

Cistanche deserticola (C. deserticola) is a holoparasitic plant of the Orobanchaceae family that parasitizes the roots of Haloxylon ammodendron (H.ammodendron). The absence of a high-quality genome has impeded our understanding of its parasitic mechanisms. Here, we present a chromosome-level genome assembly of C. deserticola (6.26 Gb) based on PacBio high fidelity (HiFi) and high-throughput chromosome conformation capture (Hi-C) sequencing, with a contig N50 of 81.25 Mb, 92.2% Benchmarking Universal Single-Copy Ortholog (BUSCO) completeness, and 54 640 protein-coding genes. Evolutionary analysis shows that C. deserticola diverged from related Orobanchaceae species approximately 38.23 million years ago. Among its key parasitic adaptations is the extensive loss of photosynthetic genes, which is compensated by the retention of transporters and carbon metabolic pathways for the utilization of host-derived nutrition. Bidirectional genetic exchanges include 34 H. ammodendron-derived horizontally transferred genes and 98 mobile mRNAs, as well as 14 C. deserticola-derived horizontally transferred genes and 77 mobile mRNAs targeting host defenses. Spatial transcriptomic data reveal haustorium-specific gene expression related to nutrient extraction and chemical defense, particularly the biosynthesis of phenylethanoid glycosides via dispersed-duplication-driven gene expansion. This genomic resource illuminates the evolutionary trajectory of C. deserticola and provides a foundation for conservation strategies and the biotechnological development of C. deserticola.