Complete chloroplast genome analysis of critically endangered endemic Prangos denticulata and insights into its evolutionary dynamics
Prangos denticulata (Apiaceae) is a critically endangered and narrowly endemic species restricted to Ankara, Türkiye. To provide genomic resources for its conservation and evolutionary study, we sequenced, assembled, and annotated its complete chloroplast genome using short-read next-generation sequencing. The circular plastome was 153,486 bp in length, exhibiting the typical quadripartite structure with a large single-copy (86,440 bp), small single-copy (17,894 bp), and two inverted repeats (49,152 bp), and an overall GC content of 37.8%. A total of 116 genes were identified, including 92 protein-coding, 31 tRNA, and 5 rRNA genes, of which 20 contained introns. Comparative analyses with P. trifida, P. lipskyi, and P. fedtschenkoi revealed high structural conservation with lineage-specific variation at the Inverted Repeat/Small Single Copy boundaries and within ndh regions. Nucleotide diversity analysis identified several highly variable coding and intergenic regions with potential utility as molecular markers. Codon usage analysis showed a strong bias toward A/U-ending codons and moderate selection pressure influencing synonymous codon choice. Phylogenomic reconstruction based on complete chloroplast genomes confirmed P. denticulata as a distinct lineage forming a well-supported clade with P. trifida, closely related to Apium graveolens. This study provides the first complete plastome of P. denticulata, expanding genomic resources for the genus Prangos and offering valuable insights into its evolutionary dynamics, systematics, and future conservation strategies.