The complete chloroplast genome of Hedera helix (Araliaceae): comparative plastome analyses reveal divergence hotspots, selective constraints, and phylogenetic placement

Abstract

Background Hedera helix: is an ecologically, horticulturally, and medicinally important member of Araliaceae. Although a genome sequence of this species has been reported, detailed chloroplast genome annotation and focused comparative plastome analysis of H. helix remain limited. This study aimed to assemble and annotate the complete chloroplast genome of H. helix and to evaluate its structural features, sequence variation, and phylogenetic position in a comparative family-level context. Methods Approximately 22 Gb of Illumina 150 bp paired-end data were generated for H. helix. The complete chloroplast genome was assembled de novo and annotated using standard plastome assembly and annotation pipelines. Comparative analyses included genome structure characterization, repeat and simple sequence repeat (SSR) detection, codon usage analysis, IR/SC boundary comparison, nucleotide diversity scanning, synteny assessment, and plastome-based phylogenetic reconstruction using representative Araliaceae taxa. Results The H. helix plastome is 156,688 bp in length and exhibits the typical quadripartite structure, comprising a large single-copy region of 86,626 bp, a small single-copy region of 18,180 bp, and two inverted repeats of 25,941 bp each, with an overall GC content of 37.99%. A total of 132 genes were annotated, including 87 protein-coding genes, 37 tRNAs, and 8 rRNAs. Repeat analyses identified 54 long repeats and 47 SSRs, most of which were A/T-rich. Codon usage analysis revealed a preference for codons ending in A or T. Comparative analyses showed that plastome structure and gene order were highly conserved across sampled Araliaceae species, with only minor variation at IR/SC junctions. Most protein-coding genes had Ka/Ks ratios consistent with purifying selection, whereas nucleotide diversity analysis identified several localized divergence hotspots, particularly in ycf1. Phylogenomic analysis based on plastome data strongly supported H. helix as sister to (H. rhombea + H. nepalensis var. sinensis). Conclusion This study provides a complete and curated plastome resource for H. helix and shows that its chloroplast genome is structurally conserved relative to other sampled Araliaceae plastomes. The identified SSRs and highly variable regions, especially ycf1, represent potential candidates for future marker development. In addition, the plastome-based phylogenetic results provide useful evidence for evaluating the placement of Hedera within Araliaceae.