Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
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
_version_ 1783422475638407168
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
work_keys_str_mv AT leehyunoh dynamicchloroplastgenomerearrangementanddnabarcodingforthreeapiaceaespeciesknownasthemedicinalherbbangpoong
AT johhojun dynamicchloroplastgenomerearrangementanddnabarcodingforthreeapiaceaespeciesknownasthemedicinalherbbangpoong
AT kimkyunghee dynamicchloroplastgenomerearrangementanddnabarcodingforthreeapiaceaespeciesknownasthemedicinalherbbangpoong
AT leesangchoon dynamicchloroplastgenomerearrangementanddnabarcodingforthreeapiaceaespeciesknownasthemedicinalherbbangpoong
AT kimnamhoon dynamicchloroplastgenomerearrangementanddnabarcodingforthreeapiaceaespeciesknownasthemedicinalherbbangpoong
AT parkjeeyoung dynamicchloroplastgenomerearrangementanddnabarcodingforthreeapiaceaespeciesknownasthemedicinalherbbangpoong
AT parkhyunseung dynamicchloroplastgenomerearrangementanddnabarcodingforthreeapiaceaespeciesknownasthemedicinalherbbangpoong
AT parkmiso dynamicchloroplastgenomerearrangementanddnabarcodingforthreeapiaceaespeciesknownasthemedicinalherbbangpoong
AT kimsoonok dynamicchloroplastgenomerearrangementanddnabarcodingforthreeapiaceaespeciesknownasthemedicinalherbbangpoong
AT kwakmyounghai dynamicchloroplastgenomerearrangementanddnabarcodingforthreeapiaceaespeciesknownasthemedicinalherbbangpoong
AT kimkyuyeob dynamicchloroplastgenomerearrangementanddnabarcodingforthreeapiaceaespeciesknownasthemedicinalherbbangpoong
AT leewookyu dynamicchloroplastgenomerearrangementanddnabarcodingforthreeapiaceaespeciesknownasthemedicinalherbbangpoong
AT yangtaejin dynamicchloroplastgenomerearrangementanddnabarcodingforthreeapiaceaespeciesknownasthemedicinalherbbangpoong