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

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.