Chromosome-Level Genome Assembly of Solanum carolinense

(1) Background: Horsenettle (Solanum carolinense) is a noxious weed widely distributed across North America and increasingly invasive in other regions. Its strong environmental adaptability, complex defense strategies, and distinctive reproductive traits make it an important model for studying plant-herbivore coevolution. However, the absence of high-quality genomic resources has limited deeper investigation into its adaptive evolutionary mechanisms. (2) Methods: In this study we generated a chromosome-level reference genome assembly for S. carolinense using an integrated approach combining PacBio HiFi long-read sequencing, Illumina second-generation sequencing, and Hi-C chromosome-mapping; (3) The final genome assembly has a total length of 915.40 Mb, with a contig N50 of 51.06 Mb and a scaffold N50 of 73.17 Mb; 96.05% of the sequences were successfully mapped to 12 pseudo-chromosomes. The genome is characterized by a high proportion of repetitive sequences (73.64%) and substantial heterozygosity (1.13%), consistent with a highly repetitive and highly heterozygous genome. BUSCO analysis indicates a completeness of 94.7%. A total of 32,206 protein-coding genes were annotated, of which 97.95% received functional annotations; (4) Conclusions: This reference genome provides a valuable resource for advancing research on the adaptive evolution of Solanaceae weeds, supports the development of more effective management strategies for this troublesome species, and offers a technical reference for assembling other highly heterozygous weed genomes.