Comparative chloroplast genomes of Paris Sect. Marmorata: insights into repeat regions and evolutionary implications

Xiaoyang Gao,Honghu Meng,Xuan Zhang,Changning Liu,Di Zhang,Jing Li

doi:10.1186/s12864-018-5281-x

Abstract

BackgroundSpecies of Paris Sect. Marmorata are valuable medicinal plants to synthesize steroidal saponins with effective pharmacological therapy. However, the wild resources of the species are threatened by plundering exploitation before the molecular genetics studies uncover the genomes and evolutionary significance. Thus, the availability of complete chloroplast genome sequences of Sect. Marmorata is necessary and crucial to the understanding the plastome evolution of this section and facilitating future population genetics studies. Here, we determined chloroplast genomes of Sect. Marmorata, and conducted the whole chloroplast genome comparison.ResultsThis study presented detailed sequences and structural variations of chloroplast genomes of Sect. Marmorata. Over 40 large repeats and approximately 130 simple sequence repeats as well as a group of genomic hotspots were detected. Inverted repeat contraction of this section was inferred via comparing the chloroplast genomes with the one of P. verticillata. Additionally, almost all the plastid protein coding genes were found to prefer ending with A/U. Mutation bias and selection pressure predominately shaped the codon bias of most genes. And most of the genes underwent purifying selection, whereas photosynthetic genes experienced a relatively relaxed purifying selection.ConclusionsRepeat sequences and hotspot regions can be scanned to detect the intraspecific and interspecific variability, and selected to infer the phylogenetic relationships of Sect. Marmorata and other species in subgenus Daiswa. Mutation and natural selection were the main forces to drive the codon bias pattern of most plastid protein coding genes. Therefore, this study enhances the understanding about evolution of Sect. Marmorata from the chloroplast genome, and provide genomic insights into genetic analyses of Sect. Marmorata.

Highlights

IntroductionMarmorata are valuable medicinal plants to synthesize steroidal saponins with effective pharmacological therapy
Comparison of gene contents revealed that two genes were unique to chloroplast genomes sequenced in this study, and another four genes were unique to chloroplast genomes sequenced by Huang et al, respectively (Additional file 2: Figure S1)
The chloroplast genomes exhibit a typical quadripartite structure of Large single copy (LSC) and Small single copy (SSC) regions separated by a pair of Inverted repeat (IR), and they share similar features in the terms of gene organization and AT-rich content

Summary

Introduction

Marmorata are valuable medicinal plants to synthesize steroidal saponins with effective pharmacological therapy. The wild resources of the species are threatened by plundering exploitation before the molecular genetics studies uncover the genomes and evolutionary significance. The availability of complete chloroplast genome sequences of Sect. Marmorata is necessary and crucial to the understanding the plastome evolution of this section and facilitating future population genetics studies. The species of Paris are famous herbal essence for the elements like steroidal saponins with effective pharmacological therapy. We selected the rare species of the genus Paris Section Marmorata H. Li to explore the chloroplast genome analyses. Marmorata comprises two species of perennial medicinal herbs, i.e., P. marmorata Stearn and P. luquanensis H.

Methods

Results

Conclusion