First chloroplast genome sequence of a critically endangered and high-value Himalayan medicinal herb Aconitum heterophyllum (Atis) directed its phylogenomic placement within the genus

Introduction Aconitum heterophyllum , a member of family Ranunculaceae, is a critically endangered Himalayan medicinal herb widely used in traditional Indian medicine for its pharmacological properties, including anti-inflammatory, analgesic, and cardioprotective effects. Despite its medicinal importance and conservation priority, genomic resources for this species remain scarce. Methods This study reports the first and complete chloroplast genome of A. heterophyllum , assembled de novo using Oxford Nanopore long-read sequencing, enriching genomic resources for the genus Aconitum . Results The circular genome is 157,327 bp in length with a GC content of 37.96%, exhibiting the typical quadripartite structure comprising a large single-copy (LSC) region (87,803 bp), a small single-copy (SSC) region (17,102 bp), and two inverted repeats (IRs) of ~26.2 kb each. The genome encodes 124 genes, including 83 protein-coding genes, 34 tRNAs, and 7 rRNAs. Codon usage analysis revealed a bias toward A/T-ending codons, with overall weak codon usage bias. Phylogenetic reconstruction using 74 core chloroplast genes from 65 Aconitum genomes identified A. coreanum as the closest plastome-level relative of A. heterophyllum , while nuclear ITS evidence suggests affinity with A. polycarpum , supporting its placement within subgenus Aconitum and section Sinaconitum, consistent with previous morphological and phytochemical classification. Discussion This study provides a high-quality chloroplast genome resource that complements existing phylogenomic frameworks and supports future studies on molecular identification and conservation genetics of Aconitum species.