A new map of the chloroplast genome of Hippophae based on inter- and intraspecific variation analyses of 13 accessions belonging to eight Hippophae species

Sea buckthorn ( Hippophae rhamnoides L.; Elaeagnaceae) is a medicinally and ecologically important deciduous shrub widely distributed in northwest China. Hybrid breeding plays an important role in the sea buckthorn industry. However, limited research has been conducted on its chloroplast genome, and data on interspecific and intraspecific variation is also lacking, which hinders the improvement in hybrid breeding. In this study, we sequenced the chloroplast (cp) genomes of seven Hippophae rhamnoides L . plants using Illumina paired-end sequencing. The cp genome of Hippophae rhamnoides L . is 155, 260–156, 312 bp in length and is composed of a large single-copy (LSC) region (83,026–84,034 bp) and a small single-copy (SSC) region (18,732–19,048 bp), which are separated by a pair of inverted repeats (IR) regions (26,653–26,670 bp). Each cp genome contains 113 genes and has a highly conserved genome structure and gene sequence. We analyzed the nucleotide diversity of the cp genomes of 13 accessions belonging to eight Hippophae species. A total of 2,838 variable sites and two hotspot maps were obtained by intra- and interspecies analyses and used to construct a map of the genome. A phylogenetic analysis was used to analyze the origin and evolution of H.rhamnoides subsp. mongolica and its related species for the first time. This study provides the basis for the identification and hybrid breeding of Hippophae species and lays the foundation for future research.