Whole Chloroplast Genome Characterization and Comparison of Two Sympatric Species in Genus <em>Hippophae</em> (Elaeagnaceae)

Abstract

Hippophae is a tree species with ecological, economic and social benefits. In this study, we assembled and annotated chloroplast genomes of sympatric Hippophae gyantsensis and H. rhamnoides subsp. yunnanensis. Their full-length are 155260 and 156415 bp, respectively. Each of them has 131 genes, comprising 85 protein-coding genes, 8 ribosomal RNA genes and 38 transfer RNA genes. After comparing the chloroplast genomes, we found 1302 base difference loci, and 63.29% are located in the intergenic region or intron sequences and 36.71% are located in the coding sequences. The SSC region has the highest mutation rate, followed by the LSC region; the IR regions have the lowest mutation rate. Among the protein-coding genes, three had a ratio of nonsynonymous to synonymous substitutions (Ka/Ks) &amp;gt;1 (but P values were non-significant) and 66 had Ka/Ks &amp;lt;1 (46 were significant). In general, the chloroplast protein-coding genes may be subject to purification selection. Among H. gyantsensis and H. rhamnoides subsp. yunnanensis chloroplast protein-coding genes, there are 20 and 16 optimal codons, respectively. Most of the optimal codons were ending with A or U, which indicates significant AT preference. It is an important reference for studies on the general characteristics and evolution of the Hippophae chloroplast genome.

Characterization of the complete chloroplast genome of Hippophae salicifolia D. Don (Elaeagnaceae)

“…Combined nuclear and plastid data resolved a clade composed of H. tibetana and H. rhamnoides with moderate to strong support (Jia and Bartish 2018 ). Nevertheless, the phylogenetic relationships among H. neurocarpa , H. gyantsensis , and H. tibetana based on 32 complete chloroplast genomes revealed H. rhamnoides was more closely related to H. neurocarpa than H. tibetana (Wang et al 2018 ; Zhou et al 2019 ; Zhou et al 2020 ). Here, we sequenced and assembled the complete chloroplast genome of H. salicifolia , and compared with other Hippophae species.…”