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Dynamic Chloroplast Genome Rearrangement and DNA Barcoding for Three Apiaceae Species Known as the Medicinal Herb “Bang-Poong”
Three Apiaceae species Ledebouriella seseloides, Peucedanum japonicum, and Glehnia littoralis are used as Asian herbal medicines, with the confusingly similar common name “Bang-poong”. We characterized the complete chloroplast (cp) genomes and 45S nuclear ribosomal DNA (45S nrDNA) sequences of two a...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6539805/ https://www.ncbi.nlm.nih.gov/pubmed/31060231 http://dx.doi.org/10.3390/ijms20092196 |
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author | Lee, Hyun Oh Joh, Ho Jun Kim, Kyunghee Lee, Sang-Choon Kim, Nam-Hoon Park, Jee Young Park, Hyun-Seung Park, Mi-So Kim, Soonok Kwak, Myounghai Kim, Kyu-yeob Lee, Woo Kyu Yang, Tae-Jin |
author_facet | Lee, Hyun Oh Joh, Ho Jun Kim, Kyunghee Lee, Sang-Choon Kim, Nam-Hoon Park, Jee Young Park, Hyun-Seung Park, Mi-So Kim, Soonok Kwak, Myounghai Kim, Kyu-yeob Lee, Woo Kyu Yang, Tae-Jin |
author_sort | Lee, Hyun Oh |
collection | PubMed |
description | Three Apiaceae species Ledebouriella seseloides, Peucedanum japonicum, and Glehnia littoralis are used as Asian herbal medicines, with the confusingly similar common name “Bang-poong”. We characterized the complete chloroplast (cp) genomes and 45S nuclear ribosomal DNA (45S nrDNA) sequences of two accessions for each species. The complete cp genomes of G. littoralis, L. seseloides, and P. japonicum were 147,467, 147,830, and 164,633 bp, respectively. Compared to the other species, the P. japonicum cp genome had a huge inverted repeat expansion and a segmental inversion. The 45S nrDNA cistron sequences of the three species were almost identical in size and structure. Despite the structural variation in the P. japonicum cp genome, phylogenetic analysis revealed that G. littoralis diverged 5–6 million years ago (Mya), while P. japonicum diverged from L. seseloides only 2–3 Mya. Abundant copy number variations including tandem repeats, insertion/deletions, and single nucleotide polymorphisms, were found at the interspecies level. Intraspecies-level polymorphism was also found for L. seseloides and G. littoralis. We developed nine PCR barcode markers to authenticate all three species. This study characterizes the genomic differences between L. seseloides, P. japonicum, and G. littoralis; provides a method of species identification; and sheds light on the evolutionary history of these three species. |
format | Online Article Text |
id | pubmed-6539805 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-65398052019-06-04 Dynamic Chloroplast Genome Rearrangement and DNA Barcoding for Three Apiaceae Species Known as the Medicinal Herb “Bang-Poong” Lee, Hyun Oh Joh, Ho Jun Kim, Kyunghee Lee, Sang-Choon Kim, Nam-Hoon Park, Jee Young Park, Hyun-Seung Park, Mi-So Kim, Soonok Kwak, Myounghai Kim, Kyu-yeob Lee, Woo Kyu Yang, Tae-Jin Int J Mol Sci Article Three Apiaceae species Ledebouriella seseloides, Peucedanum japonicum, and Glehnia littoralis are used as Asian herbal medicines, with the confusingly similar common name “Bang-poong”. We characterized the complete chloroplast (cp) genomes and 45S nuclear ribosomal DNA (45S nrDNA) sequences of two accessions for each species. The complete cp genomes of G. littoralis, L. seseloides, and P. japonicum were 147,467, 147,830, and 164,633 bp, respectively. Compared to the other species, the P. japonicum cp genome had a huge inverted repeat expansion and a segmental inversion. The 45S nrDNA cistron sequences of the three species were almost identical in size and structure. Despite the structural variation in the P. japonicum cp genome, phylogenetic analysis revealed that G. littoralis diverged 5–6 million years ago (Mya), while P. japonicum diverged from L. seseloides only 2–3 Mya. Abundant copy number variations including tandem repeats, insertion/deletions, and single nucleotide polymorphisms, were found at the interspecies level. Intraspecies-level polymorphism was also found for L. seseloides and G. littoralis. We developed nine PCR barcode markers to authenticate all three species. This study characterizes the genomic differences between L. seseloides, P. japonicum, and G. littoralis; provides a method of species identification; and sheds light on the evolutionary history of these three species. MDPI 2019-05-04 /pmc/articles/PMC6539805/ /pubmed/31060231 http://dx.doi.org/10.3390/ijms20092196 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Lee, Hyun Oh Joh, Ho Jun Kim, Kyunghee Lee, Sang-Choon Kim, Nam-Hoon Park, Jee Young Park, Hyun-Seung Park, Mi-So Kim, Soonok Kwak, Myounghai Kim, Kyu-yeob Lee, Woo Kyu Yang, Tae-Jin Dynamic Chloroplast Genome Rearrangement and DNA Barcoding for Three Apiaceae Species Known as the Medicinal Herb “Bang-Poong” |
title | Dynamic Chloroplast Genome Rearrangement and DNA Barcoding for Three Apiaceae Species Known as the Medicinal Herb “Bang-Poong” |
title_full | Dynamic Chloroplast Genome Rearrangement and DNA Barcoding for Three Apiaceae Species Known as the Medicinal Herb “Bang-Poong” |
title_fullStr | Dynamic Chloroplast Genome Rearrangement and DNA Barcoding for Three Apiaceae Species Known as the Medicinal Herb “Bang-Poong” |
title_full_unstemmed | Dynamic Chloroplast Genome Rearrangement and DNA Barcoding for Three Apiaceae Species Known as the Medicinal Herb “Bang-Poong” |
title_short | Dynamic Chloroplast Genome Rearrangement and DNA Barcoding for Three Apiaceae Species Known as the Medicinal Herb “Bang-Poong” |
title_sort | dynamic chloroplast genome rearrangement and dna barcoding for three apiaceae species known as the medicinal herb “bang-poong” |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6539805/ https://www.ncbi.nlm.nih.gov/pubmed/31060231 http://dx.doi.org/10.3390/ijms20092196 |
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