The genome of Cynanchum thesioides (Freyn) K. Schum provides insights into its systematics and candidate genes potentially associated with drought tolerance as a xerophyte

Cynanchum thesioides (Freyn) K. Schum is an important xerophytic plant, renowned for its exceptional drought resistance. However, the genetic basis of its adaptation to extreme arid environments remains largely unknown, and the candidate genes potentially involved have yet to be identified. Additionally, as a unique resource plant, this species requires clarification of its precise phylogenetic position. Analysis of the C. thesioides genome will provide critical resources for elucidating its key drought resistance mechanisms and taxonomic status. We generated a chromosome-level genome assembly of C. thesioides with a total size of 242 Mb. Phylogenetic analysis placed it within the Apocynaceae family, where it is closely related to A. pictum and C. roseus . Compared to other species in the order Gentianales, C. thesioides had significantly expanded gene families. These families were functionally enriched in pathways related to the biosynthesis of stilbenoids, phenylpropanoids, and flavonoids—processes that were commonly associated with drought responses. Additionally, integrative genomic and transcriptomic analyses revealed expression changes in genes involved in lignin biosynthesis. Notably, key gene families such as POD and Laccase showed marked clustering on chromosomes 3 and 9. In conclusion, this work provides important information on the evolutionary development of C. thesioides (Apocynaceae). It elucidates the candidate genes underlying its exceptional drought tolerance and emphasizes the importance of integrated multi-omics approaches for studying plant adaptation to environmental stress.