Study On The Evolution Of Chloroplast Genome Of Hippophae

The genus Hippophae belongs to family Elaeagnaceae,which contains seven species and11 subspecies,mainly distributing in the temperate zone of Eurasia.The classification and phylogeny within this genus have been in debate for long time.The chloroplast genome has the characteristics of small length,low nucleotide substitution rate,single parent inheritance,conserved gene content and genome structure order,etc,and thus is considered to be a powerful tool for studying phylogenetic problems.In this study,a total of chloroplast genome sequences of 37 individuals from 5 species and 8 subspecies of genus of Hippophae and one of Elaeagnus were assembled by de novo sequencing via second-generation sequencing technology.By annotating representative individuals,adaptive evolution of chloroplast genomes was analyzed for Hippophae plant;and phylogenetic trees were constructed based on all whole chloroplast genome sequences from family Elaeagnaceae.The main results of this study are as follows:(1)The chloroplast genome size of Hippophae varied between 154 983 bp and 156 514 bp,which is a typical tetrad structure,with a long single copy(LSC)region and a short single copy(SSC)Region,separated by a pair of inverted repeats(IRs).The GC content of various chloroplast genomes in Hippophae did not change much,about 36.6%-36.7%;the chloroplast genome of each species and subspecies in the genus contains 130 genes,including 84 protein coding genes,38 t RNA genes and 8 r RNA genes.A contrast of chloroplast genome between Hippophae and Elaeagnus suggested that these two genera got exactly the same chloroplast structure and gene composition,while the chloroplast genome size of the Hippophae got a limited expansion in all the LSC,SSC,and IR regions.(2)The chloroplast genome sequence among species and subspecies of Hippophae showed moderate sequence differentiation,including some high differentiation intergenic regions distributed in LSC and SSC regions.The structure and gene order of chloroplast genome among species and subspecies of Hippophae was highly conserved.RNA editing in the chloroplast genome of Hippophae occurs in the first and second positions of codons,and the latter was more common.Most of the editing site changes make the original hydrophilic amino acid into a hydrophobic amino acid,which greatly increases the hydrophobicity of the protein after editing.The branch model detected a positive selection of the ycf1 gene in H.tibetana;the site model indicated that positive selection sites exist in 23 genes coding genes of chloroplast genome of Hippophae,with the ycf1 gene got the most positive selection sites.(3)Phylogenetic trees based on the chloroplast genome complete sequences(excluded one IR region)and protein gene coding regions of 45 Hippophae and Elaeagnus individuals showed that plant from these two genus formed two single-line sister groups with high support rates.The Hippophae lineage was composed of two evolutionary branches with a high support rate: one of them included H.neurocarpa、H.salicifolia and H.gyantsensis,and the other branch included H.tibetana and all subspecies of H.rhamnoides.The two datasets are basically the same in the topological structure of the second branch: H.tibetana is located at the base of the branch;then H.rhamnoides subsp.yunnanensis is located at the most base position of the H.rhamnoides.H.rhamnoides subsp.fluviatilis and H.rhamnoides subsp.rhamnoides first gather together,and then they gather together with H.rhamnoides subsp.caucasica.These three subspecies and H.rhamnoides subsp.turkestanica gather together to form a small clade;H.rhamnoides subsp.monglica and H.rhamnoides subsp.sinensis gather together to form another small clade.However,the two sets of data sets have diverged in the analysis of the topological relationship between H.neurocarpa、H.salicifolia and H.gyantsensis and the branch support rate has decreased.This result is similar to the controversy in the previous molecular and morphological studies,indicating that the order of differentiation of these three species is not clear.Hippophae began to divergence in the Neogene Pliocene Zanclean Period about 3.30 million years ago,and the third large-scale uplift of the Qinghai-Tibet Plateau occurred from the late Pliocene to the early Quaternary,so the origin of Hippophae may be related to the third large-scale uplift of the Qinghai-Tibet Plateau and that supports the hypothesis that Hippophae originated from the Qinghai-Tibet Plateau and adjacent plateaus before moving to other northern hemisphere regions and experiencing divergence.In all,the chloroplast genome of Hippophae were highly conserved in gene composition;only a few genes might be selected by positive selection,RNA editing in the chloroplast genome of Hippophae might have greatly increases the hydrophobicity of the protein.While biological function of both positive selection and RNA editing need more experiment validation.Phylogenetic analysis based on chloroplast genome supported a monophylogenetic origin and out of Qinghai-Tibet Plateau of Hippophae.These would further help our understanding of the chloroplast genome of this genus and a deeper understanding of the evolutionary history and phylogenetic relationship of the genus.