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.

Figure 1

Gene map of Paris Chloroplast genome. The genes inside and outside of the circle are transcribed in the clockwise and counterclockwise directions, respectively. Genes belonging to different functional groups are shown in different colors. The thick lines indicate the extent of the inverted repeats (IRa and IRb) that separate the genomes into small single-copy (SSC) and large single-copy (LSC) regions.

Figure 2

Analysis of repeated sequences in the three Paris chloroplast genomes. (A) Frequency of simple sequence repeats (SSRs) by MISA. (B) Frequency of repeat sequences determined by REPuter.

Figure 3

Sliding window analysis of the whole chloroplast genome of three Paris species. (window length: 600 bp, step size: 200 bp). X-axis: position of the midpoint of a window, Y-axis: nucleotide diversity of each window.

Figure 4

NJ tree for Paris using the rbcL + matK + trnH-psbA (A) and ycf1a + ycf1b (B) DNA barcode combination. NJ topology shown with NJ/MP/ML bootstrap support values were listed at each node.