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. 2023 Jan 6:13:1099856.
doi: 10.3389/fpls.2022.1099856. eCollection 2022.

Application of chloroplast genome in the identification of Phyllanthus urinaria and its common adulterants

Hui Fang  1 , Guona Dai  1 , Binbin Liao  1 , Ping Zhou  1 , Yinglin Liu  1
Affiliations

Application of chloroplast genome in the identification of Phyllanthus urinaria and its common adulterants

Hui Fang et al. Front Plant Sci. .

Abstract

Background: Phyllanthus urinaria L. is extensively used as ethnopharmacological material in China. In the local marketplace, this medicine can be accidentally contaminated, deliberately substituted, or mixed with other related species. The contaminants in herbal products are a threat to consumer safety. Due to the scarcity of genetic information on Phyllanthus plants, more molecular markers are needed to avoid misidentification.

Methods: In this study, the complete chloroplast genome of nine species of the genus Phyllanthus was de novo assembled and characterized.

Results: This study revealed that all of these species exhibited a conserved quadripartite structure, which includes a large single copy (LSC) region and small single copy (SSC) region, and two copies of inverted repeat regions (IRa and IRb), which separate the LSC and SSC regions. And the genome structure, codon usage, and repeat sequences were highly conserved and showed similarities among the nine species. Three highly variable regions (trnS-GCU-trnG-UCC, trnT-UGU-trnL-UAA, and petA-psbJ) might be helpful as potential molecular markers for identifying P. urinaria and its contaminants. In addition, the molecular clock analysis results showed that the divergence time of the genus Phyllanthus might occur at ~ 48.72 Ma.

Conclusion: This study provides valuable information for further species identification, evolution, and phylogenetic research of Phyllanthus.

Keywords: Phyllanthus urinaria; chloroplast genome; molecular marker; phylogenetic; species identification.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Cp genomes map of Phyllanthus. Genes inside and outside the circle are transcribed clockwise and counter-clockwise.
Figure 2
Figure 2
The RSCU values of nine Phyllanthus cp genomes. Color key: the red values indicate higher RSCU values, and the blue values indicate lower RSCU values (For interpretation of the references to color in this Figure legend, the reader is referred to the web version of this article).
Figure 3
Figure 3
Comparisons of the borders of LSC, SSC, and IRa/b regions among the nine Phyllanthus cp genomes. The numbers represent the distance between the gene ends and the border sites, and the numbers below represent the length of the LSC, SSC, and IRa/b regions.
Figure 4
Figure 4
Comparison of nine cp genomes using P. amarus annotation as a reference. The vertical scale indicates the percentage of identity, ranging from 50% to 100%. The horizontal axis shows the coordinates within the cp genome. Genome regions are color-coded as exons, introns, and IGS, and the gray arrows indicate the direction of transcription of each gene. Annotated genes are displayed along the top.
Figure 5
Figure 5
Maximum likelihood phylogenetic tree based on complete cp genomes. Daphniphyllum oldhamii and D. macropodum were used as outgroups. Numbers at nodes are bootstrap support values.
Figure 6
Figure 6
Divergence times estimation based on cp genomes. The node ages are given for each node.
See this image and copyright information in PMC

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