Phylogenetic analysis and evolutionary trend inference of chloroplast genomes in Elaeagnaceae

Abstract

Abstract [Objective] The purpose of the research was to explore the evolutionary pattern of chloroplast genome in Elaeagnaceae, and to provide a basis for species identification and resource exploitation of Elaeagnaceae. [Methods] This study assembled four chloroplast genomes from Hippophae and Shepherdia, and compared the gene composition, repeats, and structural properties with the published Elaeagnaceae genomes. A phylogenetic tree was constructed based on sequences from these chloroplast genomes. The promising sites for DNA barcoding of Elaeagnaceae were identified by examining the highly divergent regions. [Results] It was found that the chloroplast genomes of each genus of Elaeagnaceae exhibited a significant degree of similarity in terms of tetrad structure and gene number and organization. Moreover, it was found that both IR regions and repeats of Hippophae and Shepherdia species tended to expand and increase more than those of Elaeagnus species. The phylogenetic tree based on chloroplast genomes from eighteen species of Elaeagnaceae showed that all Elaeagnus plants were grouped into a branch that exhibited an early differentiation, and all plants from Hippophae and Shepherdia were classified into another branch with a most recent common ancestry. Three potential DNA barcoding regions were examined with the ycf1 gene had the best effect. [Conclusion] This study revealed that the chloroplast genome structure of the Elaeagnus family had a conservative pattern. The IR regions and repeated sequence of the chloroplast genome had been extended and increased with the evolution of Elaeagnaceae. The selected DNA barcode sequences could distinguish the relationships among the genera of the family Elaeagnus and among the species within the genus Elaeagnus.

Keywords

• elaeagnaceae
• chloroplast genome
• phylogeny
• dna barcode