Chloroplast Genomes Characterization of Aconitum violaceum, Caltha palustris, and Delphinium denudatum (Ranunculaceae)

The Ranunculaceae family, encompassing approximately 2500 species across 50 genera, includes several taxa of medicinal importance. This study presents de novo assembled chloroplast (cp) genomes for three species: Aconitum violaceum Jacquem. ex Stapf, Caltha palustris L., and Delphinium denudatum Wall. ex Hook.f. & Thomson. All three cp genomes exhibited the typical angiosperm quadripartite structure—comprising a large single-copy region, a small single-copy region, and a pair of inverted repeats (IRa and IRb)—with total lengths of 154,523 bp (A. violaceum), 155,057 bp (C. palustris), and 154,228 bp (D. denudatum). Genome annotation identified 111–112 unique genes, including 77–78 protein-coding genes, 30 tRNAs, and four rRNAs. Notably, rps16 and rpl32 were absent in A. violaceum and D. denudatum, whereas infA was missing in C. palustris. Comparative analysis revealed high synteny, with no major genomic rearrangements, although minor IR boundary shifts were observed involving rps19, ycf1, and ndhF. Codon usage showed a pronounced bias toward A/T-ending codons (RSCU > 1.0), with leucine and isoleucine being the most frequently encoded amino acids. Simple sequence repeat (SSR) analysis detected 65–93 SSRs per genome, predominantly A/T-rich mononucleotide motifs. Maximum likelihood phylogenetic analysis of 76 complete cp genomes confirmed the monophyly of Aconitum L., Caltha L., and Delphinium Tourn. ex L., placing D. denudatum within Delphinium and grouping A. violaceum with Aconitum tanguticum in subgenus Aconitum. These findings provide genomic resources to support improved phylogenetic resolution, molecular evolution studies, conservation genetics, and medicinal plant research within Ranunculaceae.