• Korean Journal of Plant Resources
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• v.25 no.1
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• pp.96-104
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• 2012

Phylogenetic analyses were conducted to evaluate relationships of 7 taxa of Korean Carpesium including three outgroup (Inula britannica L., Inula germanica L., Rhanteriopsis lannginosa (DC.) Rauschert) by using ITS (internal transcribed spacer) sequences of nuclear ribosomal DNA. Phylogenetic studies used maximum parsimony, neighbor-joining and maximum likelihood methods analysis. The length of the ITS sequences was 731 bp, and the lengths of the ITS1, ITS2 and 5.8S regions were 284~297 bp, 264~266 bp and 164 bp, respectively. The total number of variable sites was 111 for the entire sequences, and a parsimony informative sites of 64 are valid. Base change appeared variously in ITS1 rather than in ITS2. As the result, Korean Carpesium were formed monophyletic group and C. abrotanoides situated as the most basal clade. The results show that C. macrocephalum is closely related with C. triste. C. rosulatum has the closest relationship with C. glossophyllum. C. cernuum is close to C. divaricatum. These results suggest that the ITS data used in this study could be useful for the phylogenetic analysis of Korean Carpesium.

• The Korea Journal of Herbology
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• v.30 no.3
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• pp.41-47
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• 2015

Objectives : Due to the morphological similarity of the pericarp and description of multi-species in National Pharmacopoeia of Korea and China, the Zanthoxylum Pericarpium is difficult to authenticate adulterant in species levels. Therefore, we introduced the sequence analysis of DNA barcode and identification of single nucleotide polymorphism(SNP) to establish a reliable tool for the distinction of Zanthoxylum Pericarpium from its adulterants. Methods : To analyze DNA barcode region, genomic DNA was extracted from twenty-four specimens of authentic Zanthoxylum species and inauthentic adulterant and the individual internal transcribed spacer regions (rDNA-ITS and ITS2) of nuclear ribosomal RNA gene were amplified using ITS1, ITS2-S2F, and ITS4 primer. For identification of species-specific sequences, a comparative analysis was performed using entire DNA barcode sequences. Results : In comparison of four Zanthoxylum ITS2 sequences, we identified 16, 4, 6, and 4 distinct species-specific nucleotides enough to distinguish Z. schinifolium, Z. bungeanum, Z. piperitum, and Z. simulans, respectively. The sequence differences were available genetic marker to discriminate four species. Futhermore, phylogenetic relationship revealed a clear classification between different Zanthoxylum species showing 4 different clusters. These results indicated that comparative analysis of ITS2 DNA barcode was an useful genetic marker to authenticate Zanthoxylum Pericarpium in species levels. Conclusions : The marker nucleotides, enough to distinguish Z. schinifolium, Z. piperitum, Z. bungeanum, and Z. simulans, were obtained at 30 SNP marker nucleotides from ITS2 sequences. These differences could be used to authenticate official Zanthoxylum Pericarpium from its adulterants as well as discriminating each four species.

• Korean Journal of Plant Taxonomy
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• v.40 no.4
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• pp.234-239
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• 2010

The taxonomy of umbel genus Sium L., Apiaceae in Korea was reviewed on the basis of molecular phylogenies derived from sequences of nuclear ribosomal DNA internal transcribed spacer (ITS) regions. The ITS sequence-derived phylogeny indicates that S. heterophyllum, endemic to Korea, is identical to S. tenue, which is known as endemic to Ussuri regions. Comparisons of sequence pairs across both spacer regions gave divergence values and revealed the identity between S. tenue and S. heterophyllum on Mt. Moonsoo. On the other hand, the ITS sequences support species delimitation of S. ternifolium, as reported recently as a new species that differs from other Sium species. The ITS sequence divergence values of 1.4 and 1.6% support species delimitation between S. serra and S. ternifolium.

• Journal of Plant Biotechnology
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• v.48 no.2
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• pp.71-76
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• 2021

Angelica is a perennial plant used widely for medicinal purposes. Information on the genetic diversity of Angelica populations is important for their conservation and germplasm utilization. Although Angelica is an important medicinal plant genus registered in South Korea, no molecular markers are currently available to distinguish individual species from other similar species in different countries, in particular, China and Japan. In this study, we developed single nucleotide polymorphism (SNP) markers derived from internal transcribed spacer regions of the nuclear ribosomal DNA to identify a distinct domestic species, Angelica gigas Nakai, via a high-resolution melting (HRM) curve analyses. We also performed HRM curve analysis of intentionally mixed genomic DNA samples from five Angelica species. Finally, we investigated A. gigas Nakai and A. sinensis using varying ratios of mixed genomic DNA templates. The SNP markers developed in this study are useful for rapidly identifying A. gigas species from different countries.

• Korean Journal of Plant Resources
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• v.24 no.4
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• pp.358-369
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• 2011

The internal transcribed spacer (ITS) regions of nuclear ribosomal DNA from genus Chrysosplenium were sequenced to address phylogenetic relationship. ITS including 5.8S sequence varied in length from 647 bp to 653 bp. Among them, 219 sites were variable sites with parsimony-informative. The aligned sequences were analyzed by maximum parsimony (MP) and neighbor-joining (NJ) methods. In the strict consensus trees of parsimony analysis, the monophyly of Chrysosplenium was supported by 100% bootstrap value. The first clade, C. pseudofauriei was at the basal position of the genus, and others formed two clades with high bootstrap support. The second clade included Ser. Pilosa and Ser. Oppositifolia and third clade included Ser. Alternifolia and Ser. Flagellifera. The NJ trees showed essentially the same topology. Finally, DNA sequences of ITS regions were useful phylogenetic marker in this genus. Based on the ITS and ridge seed morphological results, C. sphaerospermum Maxim. and C. valdepilosum (Ohwi) S.H. Kang & J.W. Han were discussed their scientific names and taxonomic positions.

• Korean Journal of Plant Resources
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• v.19 no.1
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• pp.54-58
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• 2006

The genetic analyses of Acanthopanax senticosus Harms from Korea, China and Russia, were made by comparing the internal transcribed spacer (ITS) sequences of the nuclear ribosomal DNA. The ITS region of A. senticosus was amplified by polymerase chain reaction (PCR) using the universal primers and then directly sequenced. The length of the ITS region including 162 bp 5.85 rRNA gene ranged from 608 bp (for Korean and Chinese) to 611 bp (for Russian). The G+C content of ITS region were 60.20% for Korean and Chinese plants and 60.06% for Russian plants. Sequence comparisons indicated that ITS regions of A. senticosus from Korea and China were identical, whereas the ITS sequence of A. senticosus from Russia showed 99.2% homology with the plants from Korea. Variation in sequences were attributable to 5 bp substitution such as transversion or insertion events. These results suggested that A. senticosus Harms from Korea and China were closely related in phylogenetic relationship compared to Russian. In addition, A. senticosus Harms were more similar to Kalopanax pictus than A. sessiliflorus in their ITS sequences.

• Korean Journal of Plant Taxonomy
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• v.52 no.2
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• pp.85-96
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• 2022

The plant "Hong-do-go-deul-ppae-gi" has been considered as Crepidiastrum × muratagenii, a hybrid between C. denticulatum and C. lanceolatum, based on its morphological traits and geographical distribution. To reveal the hybrid origin of Hong-do-go-deul-ppae-gi, we examined additional morphological traits of this plant and its putative parents (C. denticulatum, C. lanceolatum, C. platyphyllum) and analyzed one nuclear ribosomal internal transcribed spacer (ITS) region and four chloroplast regions (trnT-L, trnL-F, rpl16 intron, and rps16 intron). As a result of examining the morphological traits, putative hybrid individuals were classified into three types based on the habit, cauline leaf, outer phyllary, and achene beak traits. A molecular analysis found that the ITS sequences of Type 1 and Type 2 individuals showed additive species-specific sites of C. denticulatum and C. lanceolatum. Plastid sequences of Type 1 and Type 2 individuals showed C. denticulatum and C. lanceolatum sequences, respectively. However, Type 3 individuals had ITS and plastid sequences corresponding to C. denticulatum. Accordingly, Type 1 and Type 2 individuals not only share morphological traits with C. denticulatum and C. lanceolatum but also show additive species-specific sites for C. denticulatum and C. lanceolatum, and not C. platyphyllum, supporting its origin as a hybrid between C. denticulatum and C. lanceolatum. Type 3 had morphological traits similar to other hybrid types but was distinguished with respect to outer phyllaries and demonstrated some resemblance to C. denticulatum. In a molecular analysis, Type 3 was found to be identical with regard to the sequence of C. denticulatum and was judged to be an ecological variation of C. denticulatum.

• ALGAE
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• v.29 no.2
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• pp.75-99
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• 2014

A small dinoflagellate, Ansanella granifera gen. et sp. nov., was isolated from estuarine and marine waters, and examined by light microscopy, scanning electron microscopy, and transmission electron microscopy. In addition, the identity of the sequences (3,663-bp product) of the small subunit (SSU), internal transcribed spacer (ITS) region (ITS1, 5.8S, ITS2), and D1-D3 large subunit (LSU) rDNA were determined. This newly isolated, thin-walled dinoflagellate has a type E eyespot and a single elongated apical vesicle, and it is closely related to species belonging to the family Suessiaceae. A. granifera has 10-14 horizontal rows of amphiesmal vesicles, comparable to Biecheleria spp. and Biecheleriopsis adriatica, but greater in number than in other species of the family Suessiaceae. Unlike Biecheleria spp. and B. adriatica, A. granifera has grana-like thylakoids. Further, A. granifera lacks a nuclear fibrous connective, which is present in B. adriatica. B. adriatica and A. granifera also show a morphological difference in the shape of the margin of the cingulum. In A. granifera, the cingular margin formed a zigzag line, and in B. adriatica a straight line, especially on the dorsal side of the cell. The episome is conical with a round apex, whereas the hyposome is trapezoidal. Cells growing photosynthetically are $10.0-15.0{\mu}m$ long and $8.5-12.4{\mu}m$ wide. The cingulum is descending, the two ends displaced about its own width. Cells of A. granifera contain 5-8 peripheral chloroplasts, stalked pyrenoids, and a pusule system, but lack nuclear envelope chambers, a nuclear fibrous connective, lamellar body, rhizocysts, and a peduncle. The main accessory pigment is peridinin. The SSU, ITS regions, and D1-D3 LSU rDNA sequences differ by 1.2-7.4%, >8.8%, and >2.5%, respectively, from those of the other known genera in the order Suessiales. Moreover, the SSU rDNA sequence differed by 1-2% from that of the three most closely related species, Polarella glacialis, Pelagodinium bei, and Protodinium simplex. In addition, the ITS1-5.8S-ITS2 rDNA sequence differed by 16-19% from that of the three most closely related species, Gymnodinium corii, Pr. simplex, and Pel. bei, and the LSU rDNA sequence differed by 3-4% from that of the three most closely related species, Protodinium sp. CCMP419, B. adriatica, and Gymnodinium sp. CCMP425. A. granifera had a 51-base pair fragment in domain D2 of the large subunit of ribosomal DNA, which is absent in the genus Biecheleria. In the phylogenetic tree based on the SSU and LSU sequences, A. granifera is located in the large clade of the family Suessiaceae, but it forms an independent clade.

• Journal of Life Science
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• v.17 no.12
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• pp.1610-1615
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• 2007

Genus Sorbus is a long lived woody species that is primarily distributed throughout Asia and Europe. This species is regarded as very important herbal medicines in Korea and China. Sorbus commixta is primarily distributed throughout Europe. We evaluated a representative sample of the four taxa with nuclear ribosomal DNA internal transcribed spacer sequences (ITS) to estimate genetic relationships within genus. Aligned nucleotide sequences of the length of ITS1 were nearly constant within genus Sorbus varying from 219 in S. aucuparia to 218 in the rest species. Especially, the 5.8S subunit of all taxa of Sorbus was found to constant of 165 bp nucleotides. However, aligned nucleotide sequences of the length of ITS2 vary from 240 in S. sambucifolia var. pseudogrcilisto 245 in S. aucuparia. Total alignment length is 629 positions, of which 35 are parsimony-informative, 32 variable but parsimony-uninformative, and 552 constant characters. The base furtherance showed the difference to the by a total taxon: an average A and T are 17.7% and G and C are 30.4%, 34.2%, respectively. All the four taxa beginning with conserved base paired triplets emerging from single strand regions (domain I). Noteworthy, in the RNA secondary structure proposed for the three Korean Sorbus taxa RNA transcript ITS2, which shows a remarkedly well-conserved folding (domain II). When compared to the European Sorbus (S. aucuparia) of ITS2. ITS analysis may be useful in germ-plasm classification several taxa of genus Sorbus.

• Korean Journal of Plant Taxonomy
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• v.45 no.3
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• pp.243-253
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• 2015

Series Chinensis, Genus Iris, endemic to the far regions of East Asia, consists of four species and related varieties. This series is divided into two major groups (I. rossii and I. minutiaurea complex). In this study, the ITS region and matK gene sequences within nuclear ribosomal DNA and plastid DNA were analyzed in order to investigate the phylogenetic relationships among the I. minutiaurea complex (I. minutiaurea, I. odaesanensis, and I. koreana) and the taxonomic identities of a putative hybrid in Mt. Palgong. In the internal transcribed spacer (ITS1, 5.8S, and ITS2) region, a total of 106 cloned genomic sequences from three taxa were obtained to study the intragenomic polymorphisms of the ITS regions. Three taxa revealed high levels of intragenomic polymorphisms, indicative of incomplete nrDNA concerted evolution. This incomplete ITS concerted evolution in the series Chinensis may be linked to the recent species divergence and frequent interspecies hybridization of the series Chinensis. In the matK gene, three taxa were fairly separated by eleven variable sites. In eight individuals collected on Mt. Palgong, putative hybrids between I. odaesanensis and I. minutiaurea were clustered in the I. minutiaurea clade in the NJ (neighbor-joining) tree based on the matK gene. However, in the ITS tree, some of them were clustered in the I. odaesanensis clade and others were clustered in the I. minutiaurea clade. Therefore, the individuals on Mt. Palgong were formed by the hybridization between two taxa (I. odaesanensis and I. minutiaurea) and not through the lineage of I. koreana.