Comparative chloroplast genome analysis of four Hippophae rhamnoides subspecies and its phylogenetic analysis

Abstract

Abstract Sea buckthorn(Hippophae rhamnoides), a hardy deciduous shrub of the family Elaeagnaceae, grows wild at high altitudes in Asia and Europe and is known for its great nutritional, medicinal and ecological value. In this study, the chloroplast genomesof four H. rhamnoidessubspecies, H. rhamnoides subsp. mongolica ‘wulanshalin’, H. rhamnoides subsp. caucasia, H. rhamnoides subsp. sinensis ‘wucixiong’, and H. rhamnoides subsp. yunnanensis, were characterized. The results showed that the genome length of these four subspecies ranged from 157,436 bp to 157,822 bp, with a typical quadripartite structure. Comparing the genome structure of these four subspecies, it was found that the chloroplast genomes were relatively conserved, retaining the same gene order. The annotation contained a total of 132 genes in each chloroplast genomes genome, with 86 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. This study identified 14 highly differentiated regions and 423 simple sequence repeats loci, which can be used as potential molecular markers for H. rhamnoides. Meanwhile, Phylogenetic analysis showed that all Hippophae taxa were clustered in the same group and formed a sister clade with Elaeagnus taxa supported by Bayesian posterior probabilities. Among Hippophae taxa, H. gyantsensis, H. neurcar and H. salicifolia were grouped together, but H. tibetana was clustered with H. rhamnoide and the other six H. rhamnoide subspecies. The findings of this research will be useful for further studies on resource protection and the taxonomic classification of sea buckthorn.