# Comparative plastid genomics of Hippophae reveals phylogenetic relationships and provides candidate DNA markers for taxonomic identification

## TL;DR

This study compares the plastid genomes of sea buckthorn species to clarify their relationships and identify DNA markers for better species identification.

## Contribution

The study provides new plastid genome data and identifies variable regions for molecular markers in Hippophae.

## Key findings

- Phylogenomic analysis confirmed the monophyly of Hippophae and placed H. tibetana within the H. rhamnoides clade.
- 46 highly variable regions and A/T-rich repeats were identified as potential molecular markers.
- H. salicifolia showed a unique ndhF–IRb/SSC configuration in its plastid genome.

## Abstract

Sea buckthorn (Hippophae L., Elaeagnaceae) is of considerable ecological and economic importance, and primarily distributed across the Qinghai–Tibet Plateau and adjacent regions. Morphological similarity among taxa has long hindered accurate species and subspecies identification, underscoring the need for robust molecular diagnostics. This study analyzed the complete plastid genome sequences of five Hippophae species (17 accessions), including a newly assembled genome of Hippophae rhamnoides subsp. mongolica. The genomes (~ 155–156 kb) exhibited a conserved quadripartite structure comprising 85 protein-coding, eight rRNA, and 38 tRNA genes. Phylogenomic reconstruction based on 78 protein-coding genes well-resolved the interspecific relationships, confirmed the monophyly of Hippophae and H. rhamnoides, and consistently placed H. tibetana within the H. rhamnoides clade. Comparative analyses identified 46 highly variable regions and abundant A/T-rich simple sequence repeats, predominantly in intergenic spacers. Inverted repeat boundaries were largely conserved across taxa, with H. salicifolia exhibiting a distinctive ndhF–IRb/SSC configuration. These plastid genomic resources provide a robust foundation for the development of diagnostic molecular markers with direct applications in Hippophae taxonomy, phylogenetics, germplasm conservation, and targeted breeding programs.

The online version contains supplementary material available at 10.1038/s41598-026-40776-0.