• Korean Journal of Plant Taxonomy
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• v.42 no.1
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• pp.13-23
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• 2012

The trnL-F region islocated in the large single-copy region of the chloroplast genome. It consists of the trnL gene, the trnL intron, and the trnL-F IGS. Molecular evolution and phylogenetic relationships in Korean Thalictrum L. were investigated using data from the cpDNA trnL-F region. Bayesian and parsimony analyses of the data set with the gap characteristics recovered well-resolved trees that are topologically similar, with clades supported by some indels evolution. Indel events of cpDNA trnL-F in Korean Thalictrum were interpreted as phylogenetically informative characteristics. Sect. Physocarpum (excluding T. osmorhizoides) was an early-diverging group with in the genus and the remaining section formed strongly supported clades. Korean Thalictrum has various evolutionary patterns, such as the spatial distribution of the nucleotide diversity and transversion-type base substitutions in the trnL-F region.

• Journal of Life Science
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• v.21 no.10
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• pp.1452-1459
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• 2011

Citrus is a common term and genus (Citrus) of flowering plants in the rue family, Rutaceae. Citrus is believed to have originated in the part of Southeast Asia bordered by Northeastern India, Myanmar (Burma) and the Yunnan province of China. The taxonomy and systematics of the genus are complex and the precise number of natural species is unclear, as many of the named species are clonally propagated hybrids, and there is genetic evidence that even some wild, true-breeding species are of a hybrid origin. One of the most popular sequences for phylogenetic inference at the generic and infrageneric levels in plants is the chloroplast trnL-trnF region. We evaluated the seven taxa with the trnL-trnF region to estimate phenotypic relationships within the genera Citrus, Poncirus, and Fortunella in Korea. Alignment of the DNA sequences required the addition of numerous gaps. Sequence variation within Citrus was mostly due to insertion/deletion. Within the genus Citrus, C. lomonia and C. sinensis were relatives and sistered with C. aurantium in the four phylogenetic analyses (MP, ML, ME, and NJ). However, some external nodes were poorly supported.

• Korean Journal of Environment and Ecology
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• v.32 no.6
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• pp.566-574
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• 2018

The purpose of this study was to identify the phylogenetic relationships of the plants in the Korean genus Suaeda and to find out the molecular markers that could confirm the interspecies relationships in the family tree through molecular phylogenetic studies. We used the nuclear ribosomal DNA ITS and the chloroplast DNA matK, psbA-trnH, and trnL-trnF as the molecular markers. We could not distinguish between S. japonica and S. maritima and between S. maritima and S. australis in the ITS region and could not distinguish between S. japonica and S. australis with the base sequence in the psbA-trnH and trnL-trnF region. However, we analyzed the combinations of four molecular marker regions and confirmed that each of five plant species of the genus Suaeda formed the independent line. Therefore, it is considered that combinations of molecular markers would be useful for the analysis of phylogenetic relationships in the genus Suaeda. Further investigations of the ecological and morphological characteristics would be needed to understand the phylogenetic relationship and lineage diversification in the genus Suaeda.

• Korean Journal of Plant Resources
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• v.30 no.5
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• pp.522-534
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• 2017

This study was investigated genetic variation in 24 Taraxacum accessions from various regions in South Korea based on the sequences of two chloroplast DNA (cpDNA) regions (trnL-trnF and rps16-trnK). T. mongolicum, T. officinale, and T. laevigatum were triploid, and T. coreanum and T. coreanum var. flavescens were tetraploid. The trnL-trnF region in native Korean dandelions (T. mongolicum, T. coreanum, and T. coreanum var. flavescens) were ranged from 931 to 935 bp in length, and that of naturalized dandelions were ranged from 910 bp (T. officinale) to 975 bp (T. laevigatum) in length. The rps16-trnK region in T. mongolicum, T. coreanum, T. coreanum var. flavescens, T. officinale, and T. laevigatum was 882-883 bp, 875-881 bp, 878-883 bp, 874-876 bp, and 847-876 bp, respectively, in length. The sequence similarity matrix of the trnL-trnF region ranged from 0.860 to 1.00 with an average of 0.949, and that of the rps16-trnK region ranged from 0.919 to 1.000 with an average of 0.967. According to the phylogenetic analysis, the Korean native taxa and naturalized taxa were divided independent clade in two cpDNA region. T. coreanum var. flavescens clustered only with T. coreanum, and there were no significant differences in their nucleotide sequences. The finding that two accessions (T. coreanum; Jogesan, T. mongolicum; Gangyang) had a high level of genetic variation suggests their utility for breeding materials.

• Korean Journal of Plant Taxonomy
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• v.37 no.4
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• pp.477-502
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• 2007

The Aconitum alboviolaceum Kom. complex includes four controversial species described from Korea; A. albouiolaceum, A. pseudolaeue, A. longecassidatum, and A. quelpaertense. The main objective of this study was to determine the taxonomic identities and systematic relationships among the species in the A. albouiolaceum complex based on morphology, numerical analyses and DNA sequence analysis. In the present study, variations in the principal morphological characters and chloroplast DNA noncoding region sequences (psbA-trnH IGS, trnL intron, and trnL-trnF IGS) were examined for 95 individuals from 20 populations. Also, neighbor-joining analysis was adopted to infer their relationships. Morphological variation appeared to be considerably high but not to be related to geographic distribution. These morphological results suggest that reevaluation of key morphological characters are needed for the proper taxonomic treatment of the complex. The length of psbA-trnH IGS region ranged from 241 to 250 bp, that of the trnL intron from 526 to 532 bp, and that of the trnL-trnF IGS region from 466 to 472 by in all taxa. Nine haplotypes were recognized from the analysis. Seven populations shared more than two haplotypes, while other thirteen populations shared only one haplotype. In the phylogenetic analysis, the nine haplotypes formed four groups, separated A. sibiricum, one of the sister groups of the complex. There also was no distinct grouping pattern supporting the species and populations observed. These results suggest that introgression or speciation might have been involved in the formation of taxa of A. alboviolaceum complex.

• Korean Journal of Plant Taxonomy
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• v.44 no.2
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• pp.111-118
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• 2014

This study aims to define the phylogenetic relationship within Korean Pinus L. and to find the molecular markers which resolve the phylogenetic relationship in genus Pinus. cpDNA atpF-H and psbA-trnH regions were used as molecular markers. We performed the molecular phylogenetic study on 17 taxa of Pinus in Korea. The combined analyses of two gene loci showed that Korean Pinus was a monophyletic group supported by 100% BP. According to the results of separate analyses, psbA-trnH region seems to work better resolving power to clarify the phylogenetic ambiguity in Korean Pinus than those of atpF-H region. Also, we tried to checked the value and resolution of two chloroplast DNA loci on phylogenetic implications.

• Korean Journal of Plant Resources
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• v.29 no.5
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• pp.547-554
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• 2016

The genus Tilia is characterized by linear form bracts of which the lower part is attached to the peduncle of a cyme. This character is distinguished from the others genus of Malvaceae. The purpose of this study is verifying the phylogenetic relationship of genus Tilia. Phylogenetic analyses were conducted to evaluate relationships of 10 taxa of Tilia in Korea and Japan including one outgroup (Gossypium hirsutum). The molecular phylogenetic analyses were conducted with sequences based on ITS, trnL-F and rpl32-trnL region. The combined data result of ITS, trnL-F and rpl32-trnL was formed by 6 clades. T. kiusiana situated as the most basal clade. T. amurensis, T. taquetii and T. rufa are composed a clade. T. koreana, T. insularis and T. japonica was formed independent clade. T. insularis has the closest relationship with T. japonica. T. miqueliana, T. mandshurica, and T. megaphylla are composed a clade and showed a sister relationship than other species.

• Korean Journal of Plant Resources
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• v.28 no.6
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• pp.743-751
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• 2015

Reynoutria japonica and R. sachalinensis have been used as medicinal resources in Korea. However, it is difficult to identify and determine these medicinal herbs correctly because they are usually customized and purchased as the fragmented rhizomes types. To develop molecular markers for distinguishing two species, we analyzed and compared the chloroplast DNA sequences of seven loci (atpB, matK, ccD-psaI, atpF-H, trnL-trnF, psbK-I and rpl32-trnL). Among them, we found two effective SNPs in psbK-I region for R. japonica and atpF-H region for R. sachalinensis. Based on these SNP sites, we designed the new R. japonica- specific primer which is able to amplify 300 bp fragment in psbK-I region. A similar strategy was applied for the atpF-H region of R. sachalinensis. These molecular markers would be successfully applied to recognize R. japonica and R. sachalinensis.

• Journal of Plant Biotechnology
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• v.44 no.2
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• pp.135-141
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• 2017

Cudrania tricuspidata Bureau is a widely used medicinal perennial woody plant. For conservation and germplasm utilization of the plant, it is imperative to obtaining information regarding the genetic diversity of the plant populations. Although C. tricuspidata is an important medicinal plant registered in South Korea, no molecular markers are currently available to distinguish Korean-specific ecotypes from other ecotypes of different countries. In this study, we developed single nucleotide polymorphism (SNP) markers derived from chloroplast genomic sequences to identify distinct Korean-specific ecotypes of C. tricuspidata via the amplification refractory mutation system (ARMS)-PCR analyses. Molecular authentication of twelve C. tricuspidata ecotypes from different regions was performed, using DNA sequences in the trnL-F chloroplast intergenic region. The SNP markers developed in this study are useful for rapidly identifying specific C. tricuspidata ecotypes from different regions.

• Korean Journal of Medicinal Crop Science
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• v.17 no.1
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• pp.46-53
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• 2009

Schizonepeta spike (Korean name "Hyung-Gae") has been used for oriental medicinal purposes in Korea, China and Japan. In this study, twenty six "Hyung-Gae" samples were collected including nine certified Schizonepeta tenuifolia plants, and seventeen commercially marketed "Hyung-Gae" products. Chloroplast trnL-F and rDNA ITS regions of the "Hyung-Gae" samples were sequenced and used to identify whether the samples were genuine S. tenuifolia or not. As the result, the trnL-F and ITS sequences of all the "Hyung-Gae" samples were shown to be identical and it was proven that commercially available medicinal products "Hyung-Gae" are genuine S. tenuifolia. Phylogenetic tree of S. tenuifolia using the trnL-F sequences was constructed and compared with phylogenetic tree using ITS of rDNA region sequences. In these tree, S. tenuifolia was affiliated in the family Lamiaceae. It is proven that trnL-F and ITS phylogenetic trees are useful to study taxonomic position of S. tenuifolia.