The newly developed single nucleotide polymorphism (SNP) markers for a potentially medicinal plant, Crepidiastrum denticulatum (Asteraceae), inferred from complete chloroplast genome data

Khoa, Hoang Dang; Jung, Joonhyung; Hyun, JongYoung; Yoon, San-Hyun; Lim, Chaejin; Park, Keedon; Kim, Joo‐Hwan

doi:10.1007/s11033-019-04789-5

Cited by 16 publications

(8 citation statements)

References 71 publications

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“…After that, CBOL Plant Working Group compared the performance of seven leading candidate plasome DNA regions (atpF-atpH interval, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK-psbI interval and trnH-psbA interval) and recommended the 2-site combination of rbcL + matK as a plant barcode based on the evaluation of recoverability, sequence quality and species identification level 23 . The generality of medicinal plants species identification were assessed according to matK and rbcL genes 16,27,[37][38][39][40] . The molecular taxonomic identification of the Canarian oceanic hotspot was studied based on matK + rbcL 41 .…”

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confidence: 99%

The specific DNA barcodes based on chloroplast genes for species identification of Orchidaceae plants

Xiao

Tong

et al. 2021

Sci Rep

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DNA barcoding is currently an effective and widely used tool that enables rapid and accurate identification of plant species. The Orchidaceae is the second largest family of flowering plants, with more than 700 genera and 20,000 species distributed nearly worldwide. The accurate identification of Orchids not only contributes to the safe utilization of these plants, but also it is essential to the protection and utilization of germplasm resources. In this study, the DNA barcoding of 4 chloroplast genes (matK, rbcL, ndhF and ycf1) were used to provide theoretical basis for species identification, germplasm conservation and innovative utilization of orchids. By comparing the nucleotide replacement saturation of the single or combined sequences among the 4 genes, we found that these sequences reached a saturation state and were suitable for phylogenetic relationship analysis. The phylogenetic analyses based on genetic distance indicated that ndhF and ycf1 sequences were competent to identification at genus and species level of orchids in a single gene. In the combined sequences, matK + ycf1 and ndhF + ycf1 were qualified for identification at the genera and species levels, suggesting the potential roles of ndhF, ycf1, matK + ycf1 and ndhF + ycf1 as candidate barcodes for orchids. Based on the SNP sites, candidate genes were used to obtain the specific barcode of orchid plant species and generated the corresponding DNA QR code ID card that could be immediately recognized by electronic devices. This study provides innovative research methods for efficient species identification of orchids. The standardized and accurate barcode information of Orchids is provided for researchers. It lays the foundation for the conservation, evaluation, innovative utilization and protection of Orchidaceae germplasm resources.

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confidence: 99%

The specific DNA barcodes based on chloroplast genes for species identification of Orchidaceae plants

Xiao

Tong

et al. 2021

Sci Rep

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“…Some regions of the plastomes of the eight Aster species showed high sequence divergence and might be used for phylogenetic reconstruction. However, these regions are different from the phylogenetic markers previously reported for Asteraceae (Do et al, 2019). Therefore, the complete chloroplast genome sequences and molecular markers might provide fundamental data for further studies on genus of Aster and related species in tribe Astereae.…”

Section: Figurementioning

confidence: 70%

“…In addition, the complete sequences of chloroplast genomes are commonly used for phylogenetic reconstruction at lower taxonomic levels, e.g., within genus, and population genetic analyses in plants. The utilization of complete chloroplast genomes has become widespread as an efficient tool for molecular phylogenetics in Aster (Kumar et al, 2009;Choi and Park, 2015;Zhang et al, 2015;Shen et al, 2017;Wang et al, 2019;Zhang et al, 2019a;Zhang X. et al, 2021;Duan et al, 2022;Palazzesi et al, 2022;Wang and Liu, 2023) and other tribes of Asteraceeae (Vargas et al, 2017;Do et al, 2019;Tyagi et al, 2019;Zhang et al, 2019b;Yu et al, 2022;Liu et al, 2023). Previous studies on Aster classification used one to several molecular markers, such as ITS, ETS, trnL-F, and psbA-trnH sequences (Li et al, 2012;Jafari et al, 2015), and some studies used only ITS sequences (Korolyuk et al, 2015), leaving many phylogenetic and taxonomic questions unresolved.…”

Section: Introductionmentioning

confidence: 99%

Insights into comparative genomics, structural features, and phylogenetic relationship of species from Eurasian Aster and its related genera (Asteraceae: Astereae) based on complete chloroplast genome

Chen,

Li,

Chen

et al. 2024

Front. Plant Sci.

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Aster L. is an economically and phylogenetically important genus in the tribe Astereae. Here, the complete plastomes of the eight Aster species were assembled and characterized using next-generation sequencing datasets. The results indicated the complete plastomes of Aster had a quadripartite structure. These genomes were 152,045–152,729 bp in length and contained 132–133 genes, including 87 protein-coding genes, 37–38 tRNA genes, and eight rRNA genes. Expansion or contraction of inverted repeat regions and forward, palindromic, complement, and reverse repeats were detected in the eight Aster species. Additionally, our analyses showed the richest type of simple sequence repeats was A/T mononucleotides, and 14 highly variable regions were discovered by analyzing the border regions, sequence divergence, and hotspots. Phylogenetic analyses indicated that 27 species in Astereae were clustered into six clades, i.e., A to D, North American, and outgroup clades, and supported that the genera Heteropappus, Kalimeris, and Heteroplexis are nested within Aster. The results indicated the clades B to D might be considered as genera. Divergence time estimate showed the clades A, B, C, and D diverged at 23.15 Mya, 15.13 Mya, 24.29 Mya, and 21.66 Mya, respectively. These results shed light on the phylogenetic relationships of Aster and provided new information on species identification of Aster and its related genera.

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“…The following sequences were used: Crepidiastrum denticulatum MK622902 (Do et al. 2019 ), Crepidiastrum lanceolatum MK358413 (Kim et al., 2019 ), lapsanastrum humile MK358416, Strebbinsia umbrella MN822134 (Lv et al. 2020 ), taraxacum mongolicum KU736961 (Kim et al.…”

Section: Resultsmentioning

confidence: 99%

The complete chloroplast genome of Elephantopus scaber L. (Vernonioideae, Asteraceae), a useful ethnomedicinal plant in asia

Nguyen,

Khang,

Nguyen

et al. 2023

Mitochondrial DNA Part B

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Elephantopus scaber L. is a useful medicinal plant and has been used as a traditional medicine for various diseases in Asia. In this study, we completed and characterized the chloroplast genome of E. scaber of which the length was 152,375 bp. This circular genome had a large-single copy (LSC, 83,520 bp), a small-single copy (SSC, 18,523 bp), and two inverted repeat regions (IR, 25,166 bp). There were 80 protein-coding genes, 30 tRNA genes, and four rRNA genes in the chloroplast genome of E. scaber . Phylogenetic analysis inferred from 80 protein-coding regions revealed a close relationship between E. scaber and Cyanthillium cinereum (L.) H.Rob. and a sister relationship between Vernonioideae and Cichorioideae subfamilies. The genomic data of E. scaber provide useful information to explore the molecular evolution of not only Elephantopus genus but also the Asteraceae family.

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The newly developed single nucleotide polymorphism (SNP) markers for a potentially medicinal plant, Crepidiastrum denticulatum (Asteraceae), inferred from complete chloroplast genome data

Cited by 16 publications

References 71 publications

The specific DNA barcodes based on chloroplast genes for species identification of Orchidaceae plants

The specific DNA barcodes based on chloroplast genes for species identification of Orchidaceae plants

Insights into comparative genomics, structural features, and phylogenetic relationship of species from Eurasian Aster and its related genera (Asteraceae: Astereae) based on complete chloroplast genome

The complete chloroplast genome of Elephantopus scaber L. (Vernonioideae, Asteraceae), a useful ethnomedicinal plant in asia

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