Intraspecific genetic variation of the hairy-fruited eggplant (Solanum lasiocarpum Dunal.) based on plastid genome sequences

Abstract Solanum lasiocarpum Dunal. is a medicinal plant with medicinal properties for minor human diseases. To generate additional genomic resources for this species, we sequenced and characterised plastomes from seven S. lasiocarpum accessions collected in Malaysia, Indonesia, and Thailand. The seven plastomes range from 155,616 to 156,854 bp and each contains 128 genes. We identified 43–46 simple sequence repeats and 32–37 long repeats per plastome, with a strong bias towards A/T-rich motifs. Two indels and three highly variable regions ( pet A, pet A– psb J, rpl 32– trn L-UAG) were detected. The intraspecific pairwise distance between the previously published Hainan accession, SLHN (GenBank accession no.: PP234975), and the seven new accessions was 0.001. Phylogenetic analyses based on both complete plastomes and protein-coding sequences (CDS) recovered SLHN as the earliest-diverging lineage, followed by a split into two major clades. In the plastome-tree, the Mantin (SLMT), Serian (SLSR), and Phukhieo (SLTH) accessions formed one clade, whereas the Lachau (SLLC), Pontianak (SLPT), Sibu (SLSB), and Sibu wild (SLSW) accessions grouped together. In the CDS-tree, SLMT and SLTH clustered together, separate from the SLLC + SLPT + SLSR + SLSB + SLSW clade. Most internal branches received low statistical support in both trees. These results provide new insights into intraspecific plastome variation in S. lasiocarpum and establish a comparative framework to support marker development, molecular breeding, and future phylogenetic and evolutionary studies in Solanum .