The complete chloroplast genome of the rare species Epimedium tianmenshanensis and comparative analysis with related species

Abstract

Epimedium tianmenshanensis is a rare perennial herb distributed in China, and it is also an important medicinal plant. Here, we used illumina paired-end sequencing technology to obtain the complete chloroplast genome of E. tianmenshanensis, and compared analysis with related species. The length of the complete chloroplast genome of E. tianmenshanensis is 156,956 bp, which is a relatively conserved quadripartite structure including a large single copy (LSC) region of 88,409 bp, a small single copy (SSC) region of 17,448 bp, and a pair of inverted repeat (IRa/IRb) regions of 25,550 bp. The whole genome contains 132 unique genes, including 85 protein-coding genes, 38 tRNA genes, eight rRNA genes and one pseudogene. 87 simple sequence repeats (SSRs) were identified, and most of them were found to be composed of A/T. In addition, 22,923 codons were detected in 78 protein-coding genes of E. tianmenshanensis, and the overall codon bias pattern in the genome tended to use A/U ending codons. Phylogenetic analysis demonstrated that all the Epimedium species formed a monophyletic clade, and E. tianmenshanensis had the closest relationship to E. dolichostemon. The results of this study provided useful molecular information about the evolution and molecular biology of E. tianmenshanensis.

Keywords: Chloroplast genome; Epimedium; Phylogenetic analysis; RSCU; SSRs.

Fig. 1

Chloroplast genome map of E. tianmenshanensis. Genes drawn inside the circle are transcribed clockwise, genes outside are transcribed counterclockwise. Genes are color coded by their function in the legend. The area in darker gray and lighter gray in the inner circle indicates GC content and AT content, respectively

Fig. 2

The frequency of codons for protein-coding genes in the chloroplast genomes of seven Epimedium plants

Fig. 3

Codons with RSCU values greater than 1 based on 78 protein-coding genes in the chloroplast genome of E. tianmenshanensis and six related species

Fig. 4

Numbers and types of SSR in the chloroplast genomes of E. tianmenshanensis

Fig. 5

Types and numbers of repeat in the chloroplast genomes of seven plastomes of Epimedium. a Numbers and types of SSR. b total of the three repeat types

Fig. 6

The partitioned Bayesian phylogenetic tree based on nine complete chloroplast genome sequences. Parsimony bootstrap values (before the slash markers) higher than 50% and Bayesian posterior probabilities (after the slash markers) more than 0.95 were indicated along branches