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

Abstract

BackgroundPhyllanthus 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.MethodsIn this study, the complete chloroplast genome of nine species of the genus Phyllanthus was de novo assembled and characterized.ResultsThis 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.ConclusionThis study provides valuable information for further species identification, evolution, and phylogenetic research of Phyllanthus.

Comparative analysis of medicinal plants Scutellaria baicalensis and common adulterants based on chloroplast genome sequencing

“…Several molecular studies have demonstrated the high identification capability of cp genetic markers in distinguishing Phyllanthus and Isodon species [ 15 , 28 ]. Four regions ( matK-rps16 , ndhC-trnV-UAC , psbE-petL , and rps16-trnQ-UUG ) have been filtered as candidate molecular markers for discriminating S. baicalensis from its common adulterants in this study.…”

“…NGS QC Toolkit v. 2.3.3 software was utilized to obtain clear reads by trimming paired-end sequence reads. De novo assemblies and annotation of the cp genomes were performed by using GetOrganelle v. 1.6.4 and online tools CpGAVAS2 [ 13 , 39 ] and GeSeq [ 28 , 40 ] with the parameter sets referred to previous studies [ 15 , 41 ], respectively. The Apollo rectified intron/exon boundaries and start/stop codons [ 9 , 42 ].…”

“…MEGA X was employed to create a molecular clock tree [ 53 ]. The relevant divergence time was then estimated through the TimeTree Resource ( http://www.timetree.org/ ) [ 28 , 54 ]. Three calibration nodes were employed: (F1) a median time of 2.85-3.85 million years ago (Mya) for the most recent common ancestor (MRCA) of S. amoena and S. baicalensis ; (F2) a median time of 2.85-3.85 Mya for the common ancestor of S. baicalensis and S. barbata ; and (F3) a median time of 0.11-1.11 Mya for the common ancestor of S. barbata and S. indica .…”

Comparative study on chloroplast genomes of three Hansenia forbesii varieties (Apiaceae)

“…The total DNA was extracted using a small plant DNA Extraction Kit (Omega Bio-Tek, USA). Then we randomly broke qualified DNA samples using an ultrasonic crusher (Covaris, USA), and then completed the whole library preparation through the steps of end repair, adding A-tailing, adding sequencing connector, purification, and PCR amplification [ 21 ]. The qualified library was sequenced using the Illumina high-throughput sequencing platform (Illumina, NovaSeq 6000, USA).…”

The complete chloroplast genome, DNA barcoding, and taxonomic notes of Swertiabanzragczii and Swertia marginata (Gentianaceae) in Mongolia

“…The development of barcoding markers has greatly advanced our understanding of the relationships between morphologically similar species; however, it has been revealed that Swertia is strongly paraphyletic to other genera within the Gentianaceae family (Chassot et al 2001; Xi et al 2014). Recently, the chloroplast genome has been widely used in plant system evolution, related species identi cation, genetic diversity analysis, chloroplast genetic engineering, and other applications due to the development of high-throughput sequencing technology (Yang et al 2016;Li et al 2021;Fang et al 2023;Nyamgerel et al 2023). The chloroplast genome (plastome) has a conserved structure, encodes 120-130 genes, most of which encode part of the photosynthetic apparatus of the organelle (Jensen and Leister, 2014), and is maternally inherited (Wicke et al 2011).…”