Characterization of the chloroplast genome of physospermum cornubiense using next-generation sequencing technology

Chloroplast genome sequencing has become a widely used approach in recent years, providing essential insights for phylogenetic analyses, systematics, evolutionary biology, taxonomy, and population genetics. In this study, the complete chloroplast genome of Physospermum cornubiense (Apiaceae), one of only two species of the genus Physospermum and naturally distributed in Turkey, was sequenced and analyzed for the first time. Total DNA extracted from collected specimens was sequenced using next-generation sequencing technologies, and the chloroplast genome was de novo assembled and annotated. The genome was found to be circular, with a length of 156,449 bp, comprising a large single-copy region (LSC: 86,333 bp), a small single-copy region (SSC: 17,730 bp), and two inverted repeats (IRa and IRb: each 26,193 bp). It contains 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Intron analysis revealed that 14 genes possess a single intron, while ycf3 and clpP contain two introns each. Comparative genomic analysis with Pleurospermum szechenyii using mVISTA demonstrated high structural and sequence similarity. Repeats were identified with REPuter, while exon–intron structures and cis- and trans-splicing genes were visualized with CPGview. These findings provide new insights into genome organization, IR expansion/contraction, and pseudogene formation within Apiaceae. This study presents the first comprehensive characterization of the chloroplast genome of P. cornubiense. The data provide an important reference for molecular evolutionary and phylogenetic studies, comparative analyses within Apiaceae, and the development of molecular markers. Furthermore, the genomic resources generated here will support future research on the genetic diversity, evolutionary relationships, and biotechnological and pharmacological potential of the species.