Chloroplast Genomic Resource of Paris for Species Discrimination

Yun Song,Shaojun Wang,Jin Xu,Ming Fu Li,Naizhong Chen,Shuifang Zhu,Yuanming Ding

doi:10.1038/s41598-017-02083-7

Abstract

Paris is famous in China for its medicinal value and has been included in the Chinese Pharmacopoeia. Inaccurate identification of these species could confound their effective exploration, conservation, and domestication. Due to the plasticity of the morphological characteristics, correct identification among Paris species remains problematic. In this regard, we report the complete chloroplast genome of P. thibetica and P. rugosa to develop highly variable molecular markers. Comparing three chloroplast genomes, we sought out the most variable regions to develop the best cpDNA barcodes for Paris. The size of Paris chloroplast genome ranged from 162,708 to 163,200 bp. A total of 134 genes comprising 81 protein coding genes, 45 tRNA genes and 8 rRNA genes were observed in all three chloroplast genomes. Eight rapidly evolving regions were detected, as well as the difference of simple sequence repeats (SSR) and repeat sequence. Two regions of the coding gene ycf1, ycf1a and ycf1b, evolved the quickest and were proposed as core barcodes for Paris. The complete chloroplast genome sequences provide more integrated and adequate information for better understanding the phylogenetic pattern and improving efficient discrimination during species identification.

Highlights

The chloroplasts are photosynthetic organelles that provide energy to green plants
The taxonomy and species identification of the genus Paris are based on the morphological traits, but the plasticity of its morphological characteristics made the classification of Paris very complicated, most Paris species have abundant intraspecific variations in morphology and chemical composition[12, 14, 15]
Analysis based on plastid genomic markers and nuclear gene ITS2 suggested that ITS2 can only discriminate P. polyphylla var. yunnanensis from P. polyphylla var. chinensis[16,17,18,19]

Summary

Introduction

The chloroplasts are photosynthetic organelles that provide energy to green plants. In angiosperms, most chloroplast genomes are circular, double-stranded DNA, containing a pair of inverted repeats (IRs), one large single-copy region (LSC) and one small single copy region (SSC)[1, 2]. The taxonomy and species identification of the genus Paris are based on the morphological traits, but the plasticity of its morphological characteristics made the classification of Paris very complicated, most Paris species have abundant intraspecific variations in morphology and chemical composition[12, 14, 15] Molecular methods, such as molecular marker techniques and DNA barcoding, provide effective information for taxonomy and species identification. Ji et al tested the generic and infrageneric circumscription of Paris with nuclear ITS and plastid psbA-trnH, trnL-trnF DNA sequence data and supported the classification of Paris as a single genus, but the delimitation of species still remained unresolved[12] All these studies have provided valuable insights for an initial molecular-based identification of Paris, but there were too little variations in those chloroplast genomic markers to address the issues of species discrimination

Objectives

Methods

Results