Characterization and comparison of chloroplast genomes from two sympatric Hippophae species (Elaeagnaceae)

The genus Hippophae includes deciduous shrubs or small trees, which provide many ecological, economic, and social benefits. We assembled and annotated the chloroplast genomes of sympatric Hippophae gyantsensis (Rousi) Lian and Hippophae rhamnoides Linn subsp. yunnanensis Rousi and comparatively analyzed their sequences. The full-length chloroplast genomes of H. gyantsensis and H. rhamnoides subsp. yunnanensis were 155,260 and 156,415 bp, respectively; both featured a quadripartite structure with two copies of a large inverted repeat (IR) separated by small (SSC) and large (LSC) single-copy regions. Each Hippophae chloroplast genome contained 131 genes, comprising 85 protein-coding, 8 ribosomal RNA, and 38 transfer RNA genes. Of 1302 nucleotide substitutions found between these two genomes, 824 (63.29%) occurred in the intergenic region or intron sequences, and 478 (36.71%) were located in the coding sequences. The SSC region had the highest mutation rate, followed by the LSC region and IR regions. Among the protein-coding genes, three had a ratio of nonsynonymous to synonymous substitutions (Ka/Ks) > 1 yet none were significant, and 66 had Ka/Ks < 1, of which 46 were significant. We found 20 and 16 optimal codons, most of which ended with A or U, for chloroplast protein-coding genes of H. gyantsensis and H. rhamnoides subsp. yunnanensis, respectively. Phylogenetic analysis of five available whole chloroplast genome sequences in the family Elaeagnaceae-using one Ziziphus jujube sequence as the outgroup-revealed that all five plant species formed a monophyletic clade with two subclades: one subclade consisted of three Hippophae species, while the other was formed by two Elaeagnus species, supported by 100% bootstrap values. Together, these results suggest the chloroplast genomes among Hippophae species are conserved, both in structure and gene composition, due to general purifying selection; like many other plants, a significant AT preference was discerned for most protein-coding genes in the Hippophae chloroplast genome. This study provides a valuable reference tool for future research on the general characteristics and evolution of chloroplast genomes in the genus Hippophae.

Automated summary

This study focused on assembling, annotating, and comparing the chloroplast genomes of Hippophae gyantsensis and H. rhamnoides subsp. yunnanensis, revealing their conserved structure and gene composition with different mutation rates in intergenic and coding sequences. Phylogenetic analysis showed a monophyletic clade formed by Hippophae species due to general purifying selection, suggesting a significant AT preference in protein-coding genes.