Chloroplast Genomes Characterization of <i>Aconitum violaceum</i> , <i>Caltha palustris</i> , and <i>Delphinium denudatum</i> (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: <i>Aconitum violaceum</i> Jacquem. ex Stapf, <i>Caltha palustris</i> L., and <i>Delphinium denudatum</i> 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 (<i>A. violaceum</i>), 155,057 bp (<i>C. palustris</i>), and 154,228 bp (<i>D. denudatum</i>). Genome annotation identified 111-112 unique genes, including 77-78 protein-coding genes, 30 tRNAs, and four rRNAs. Notably, <i>rps16</i> and <i>rpl32</i> were absent in <i>A. violaceum</i> and <i>D. denudatum</i>, whereas <i>infA</i> was missing in <i>C. palustris</i>. Comparative analysis revealed high synteny, with no major genomic rearrangements, although minor IR boundary shifts were observed involving <i>rps19</i>, <i>ycf1</i>, and <i>ndhF</i>. 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 <i>Aconitum</i> L., <i>Caltha</i> L., and <i>Delphinium</i> Tourn. ex L., placing <i>D. denudatum</i> within <i>Delphinium</i> and grouping <i>A. violaceum</i> with <i>Aconitum tanguticum</i> in subgenus <i>Aconitum</i>. These findings provide genomic resources to support improved phylogenetic resolution, molecular evolution studies, conservation genetics, and medicinal plant research within Ranunculaceae.