Chromosome-level genome assembly of the traditional Chinese medical plant Pseudostellaria heterophylla

Pseudostellaria heterophylla (Miq.) Pax, a perennial herb belonging to the Caryophyllaceae family, demonstrates substantial pharmacological value and serves as an ideal model system for studying chasmogamous and cleistogamous (CH-CL) floral dimorphism. In this study, by integrating short-read, PacBio HiFi, Hi-C, and transcriptome sequencing data, we generated a high-quality chromosome-level genome assembly for P. heterophylla. The 2.19 Gb genome exhibits high continuity (scaffold N50 = 144.78 Mb) and completeness (97.83% BUSCO score), with 99.36% sequences anchored to 16 pseudo-chromosomes. Repeat elements constituted 79.41% of the assembled genome, with long terminal repeats accounting for 67.30%. The analysis identified 37,158 protein-coding genes, of which 87.19% (32,397) received functional annotations. This high-quality genome assembly establishes a pivotal foundation for uncovering the genetic mechanisms underlying CH-CL floral differentiation and bioactive compound biosynthesis, while supporting molecular breeding initiatives for this pharmacologically valuable species.