ABSTRACT The complete chloroplast genome of Caltha scaposa , a high‐altitude wetland species native to the Himalayas and Hengduan Mountains, was assembled and characterized to clarify its phylogenetic position and explore plastome structural variation within the tribe Anemoneae. The circular genome is 160,219,155,293 bp in length and exhibits a typical quadripartite structure, including a LSC (large single copy) region of 79,994 bp, an SSC (small single copy) region of 17,075 bp, and a pair of IRs (inverted repeats) of 26,410 bp each. The genome encodes 132 genes, comprising 87 protein‐coding genes, 37 tRNA genes, and four rRNA genes. A total of 54 SSRs (simple sequence repeats) were identified, predominantly mononucleotide A/T repeats. Comparative analysis with nine related species from the genera Anemone and Pulsatilla revealed significant variation in IR boundaries. Caltha scaposa possesses the shortest IR regions, while all examined Pulsatilla species exhibit expanded IRs, resulting in structural rearrangements. Nucleotide diversity analysis indicated that intergenic spacers, especially ndhE ‐ ndhG (Pi = 0.1195), are highly variable, whereas tRNA genes are extremely conserved. Codon usage analysis revealed a bias toward A/T‐ending codons. Phylogenomic reconstruction based on 40 complete plastomes using maximum likelihood and Bayesian methods robustly placed C. scaposa as a sister lineage to the clade comprising Anemone and Pulsatilla within tribe Anemoneae. These findings clarify the systematic position of C. scaposa , highlight dynamic IR evolution in Anemoneae, and provide valuable genomic resources for future evolutionary and population genetic studies in Ranunculaceae.
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