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

作　　者：Luoyun Wang Jing Wang Caiyun He Jianguo Zhang Yanfei Zeng 

机构地区：[1]State Key Laboratory of Tree Genetics and Breeding and Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration,Research Institute of Forestry,Chinese Academy of Forestry,Beijing,People’s Republic of China [2]Collaborative Innovation Center of Sustainable Forestry in Southern China,Nanjing Forestry University,Nanjing,People’s Republic of China

出　　处：《Journal of Forestry Research》2021年第1期307-318,共12页林业研究（英文版）

基　　金：the National Natural Science Foundation of China(31670666);the Fundamental Research Funds for the Central Non-profit Research Institution of Chinese Academy of Forestry(ZDRIF201706).

摘　　要：The genus Hippophae includes deciduous shrubs or small trees,which provide many ecological,economic,and social benefi ts.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 fulllength 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 twogenomes,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 signifi-cant,and 66 had Ka/Ks<1,of which 46 were signifi cant.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 fi ve available whole chloroplast genome sequences in the family Elaeagnaceae—using one Ziziphus jujube sequence as the outgroup—revealed that all fi ve 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 signifi cant AT preference was discerned for most proteincoding genes in the Hippophae chloroplast genome.This study provides a valuable reference tool

关 键 词：Chloroplast genome Hippophae gyantsensis(Rousi)Lian Hippophae rhamnoides Linn subsp.yunnanensis Ka/Ks Optimal codon 

分 类 号：S793.6[农业科学—林木遗传育种]