Chloroplast Genomic Resource of Paris for Species Discrimination

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.

New Insights on Lilium Phylogeny Based on a Comparative Phylogenomic Study Using Complete Plastome Sequences

“…Although the nucleotide diversities of the LSC and SSC regions were higher than that of the IR region, this is a common phenomenon across the angiosperms [25]. However, the nucleotide diversities of Lilium and Fritillaria were higher in the LSC and SSC regions but lower in the IR region as compared to that of Paris belonging to Melanthiaceae of Liliales [44]. Consequently, the IR regions in Liliaceae appear to be more stable by purifying selection, and the LSC and SSC regions were assumed to have been under relaxed purifying selective pressure compared to those of Melanthiaceae during their evolutionary process.…”

Complete chloroplast genomes of Liliaceae (s.l.) species: comparative genomic and phylogenetic analyses

“…We used the codon substitution models in the Codeml program, PAML3.15 (Song et al 2017), to calculate the nonsynonymous (dN) and synonymous (dS) substitution rates, along with their ratio (ω = dN/dS). Site-specific models were employed to analyze the selection pressure on 73 common protein-coding genes.…”

Genotype classification and fluorescence visual identification of the Rhizoma Paridis of Paris polyphylla var. yunnanensis based on the SNPs of ITS sequence 

“…And the present situation has undoubtedly added great di culties to the identi cation of medicinal plants. With the unremitting efforts of predecessors such as CDDP marker , chloroplasts genome coding gene Song et al (2017), ITS2 molecular regions coupled with high resolution melting analysis , new techniques and methods for the identi cation of Paris species have been developed continuously. However, current DNA barcoding methods generally require gel electrophoresis, or sequencing and homology analysis (constructed the N-J tree) to get results, which was not so intuitive in the actual test work.…”