Haplotype-resolved genome of hexaploid Solanum nigrum: Insights into origin, evolution, and steroidal glycoalkaloid biosynthesis

Black nightshade (Solanum nigrum) is a valuable medicinal plant and emerging model for polyploid evolution, but its study is limited by the lack of a reference genome due to complex polyploidy. We present the first haplotype-resolved, chromosome-level assembly of the 6.1 Gb S. nigrum genome, organized into 12 homoeologous groups. We confirm that one diploid parent of S. nigrum is S. americanum and identify significant chromosomal rearrangements between them. Our analysis indicates that S. nigrum originated approximately 8.8 million years ago from hybridization between tetraploid and diploid progenitors followed by whole-genome duplication. Integrating multi-tissue transcriptomics, we identify 65 steroidal glycoalkaloid (SGA) biosynthesis genes that undergo sub-functionalization and neo-functionalization. We also characterize 26 core genes involved in the SGA biosynthetic pathway, establishing a framework for metabolic engineering in heterologous systems. These findings offer crucial genomic resources for advancing research, breeding, and industrial applications of S. nigrum and the broader Solanaceae family.