Chromosome-level genome assembly of Stellaria dichotoma reveals extensive transposable element proliferation in a traditional Chinese medicinal plant

Stellaria Radix, known as Yinchaihu (YCH) in traditional Chinese medicine, is derived from the dried roots of Stellaria dichotoma L. var. lanceolata Bge. Despite its clinical importance in treating pediatric febrile conditions and documented pharmacological activities, comprehensive genomic resources for this species have been unavailable. Here, we report the first chromosome-level genome assembly of YCH generated using PacBio HiFi long-read sequencing integrated with Hi-C chromatin conformation capture technology. The assembled genome spans 1.93 Gb with a contig N50 of 125.08 Mb and scaffold N50 of 133.88 Mb. Hi-C-assisted scaffolding anchored 1.93 Gb (99.98%) of assembled sequences onto 14 chromosomes, achieving 96.53% BUSCO completeness, a Long Terminal Repeat Assembly Index (LAI) of 17.04, and a quality value (QV) of 29.47, confirming high assembly quality. Genome annotation identified 48,391 protein-coding genes, with 95.51% receiving functional annotation across multiple databases. Repetitive sequences constitute 84.46% of the genome, predominantly LTR retrotransposons (67.44%), with Gypsy (39.13%) and Copia (14.18%) elements dominating. Ks distribution analysis revealed a shared ancient whole-genome duplication (WGD) event across Caryophyllaceae species, with peak LTR retrotransposon insertion activity at approximately 0.5 million years ago coinciding temporally with the WGD, suggesting polyploidy-triggered transposon proliferation. This high-quality reference genome provides essential genetic resources for elucidating the molecular mechanisms underlying the medicinal properties of YCH and will facilitate future molecular breeding, functional genomics, and pharmacological investigations of this important medicinal plant.