• Bioinformatics and Biosystems
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• v.2 no.1
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• pp.7-11
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• 2007

Methods for making scoring matrix based on phylogenetic tree for all possible exchanges of one amino acid with another. PFMT(Phylogenetic focused Mutation Tendency) matrix is different BLOSUM62 and PAM160 which are the most used scoring matrixes. This matrix calculates possibility of substitution from common ancestor to high spices. PFMT matrix scores substitution frequency in COGs databases which contain 152 KOGs's dataset. PFMT matrix usefully is able to compare between query sequence and sequences of more higher species and show detailed substitution relation of 20 amino acids.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2019.04a
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• pp.68-68
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• 2019

닥나무(Paper mulberry)는 뽕나무과(Moraceae) 닥나무속(Broussonetia)에 속하는 낙엽 활엽 관목으로 중국, 일본, 한국 등에 자생하며 Hutchinson(1967)에 의하면 닥나무 속은 열대, 아열대, 난대지방에서 자라는 낙엽성 관목으로 세계적으로 약 6종이 있다고 보고되었다. 일반적으로 닥나무의 품종을 구분하는 것은 수목학적 관점으로 잎의 성상, 줄기의 색과 무늬 유무로 구분한다. 그러나 상기의 수목학적 특징은 닥나무(Broussonetia kazinoki Siebold)와 꾸지나무[Broussonetia papyrifera (L.) L'Her. ex Vent.]가 유사하여 오동정의 사례가 발생하기도 한다. 경상도지역에서는 닥나무를 참닥나무, 머구닥나무, 개닥나무 3가지의 향명으로 구분하고 있다. 본 연구에서는 경상도지역 9개체 닥나무를 대상으로 수목학적 특징을 확인하였다. 나아가 식물종의 기준을 명확히 규명하기 위하여 엽록체 속의 matK, trnL-F, ndhF, 3개 마커와 핵에 존재하는 ITS, 총 4개 마커의 염기서열을 생산하였고 상기 구간에서 얻어진 염기서열 비교분석 및 계통학적 분류를 통해 유연관계를 파악하였다. 수목학적 관점으로는 품종을 명확하게 구분하기가 어려웠으며 분자계통학적 연구로 모든 시료는 닥나무와 꾸지나무의 교잡종으로 확인되었다. 본 연구 결과는 우리나라 전통한지의 원재료로 사용되는 닥나무류 식물자원의 분류체계의 확립을 위한 기초자료로 활용 될 것이다.

• Korean Journal of Plant Taxonomy
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• v.44 no.1
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• pp.51-58
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• 2014

This study aims to define the phylogenetic relationship within Korean section sabina and find molecular markers which resolve the phylogenetic relationship in genus Juniperus and section sabina. cpDNA matK and psbA-trnH were used as molecular markers. The combined analyses of two genes suggested that section sabina was a clade supported by 100% BP. The relationships of [J. chinensis var. sargentii+J. davurica] clade and [J. chinensis var. chinensis+J. chinensis var. procumbens+J. chinensis var. horizontalis] clade were supported by 91% BP and 100% BP, respectively. Thus, the classification of Korean section sabina would be appropriate at follows, (1) J. chinensis var. sargentii+J. davurica, and (2) J. chinensis var. chinensis+J. chinensis var. procumbens According to the results of separate analyses, matK seems to work better resolving power to clarify the phylogenetic ambiguity in Juniperus and section sabina than psbA-trnH.

• 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 Taxonomy
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• v.46 no.2
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• pp.247-255
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• 2016

As an attempt to determine the identity of the old trees of flowering cherries planted in the yard of the Catholic Archdiocese of Daegu, we conducted comparative phylogenetic analyses between wild and cultivated Prunus yedoensis Matsum. We generated the phylogeny (MP) and haplotype network (TCS) of 25 individuals, including wild P. yedoensis, from Jeju Island, cultivated P. ${\times}$yedoensis 'Somei-yoshino' from Korea and Japan, and P. spachiana f. ascendens (Makino) Kitam. from Jeju Island and Japan based on highly informative sequences of two cpDNA regions (rpl16 gene and trnS-trnG intergenic spacer). The wild and cultivated P. yedoensis were distinguished from each other in both the phylogeny and haplotype networks, and the old flowering cherry trees in Daegu had a cpDNA haplotype identical to that of the cultivated P. ${\times}$yedoensis 'Someiyoshino'. Compared to the cultivated P. ${\times}$yedoensis 'Somei-yoshino', wild P. yedoensis appears to have greater haplotype diversity, presumably originating from the genetic diversity of P. spachiana f. ascendens that functioned as a maternal parent in the hybrid origin of wild P. yedoensis. A future detailed study requires extensive sampling of P. spachiana f. ascendens from Japan and Korea to determine their precise phylogenetic relationships relative to wild and cultivated P. yedoensis. We concluded that the old flowering cherry trees planted in the yard of the Catholic Archdiocese of Daegu are highly likely to be of cultivated origin rather than wild types from Jeju Island, as previously speculated.

• Korean Journal of Plant Taxonomy
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• v.47 no.3
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• pp.222-235
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• 2017

A comparative study of the leaf epidermal micromorphology in the tribe Neillieae (Neillia: 4 species, 4 varieties; Physocarpus: 5 species; Stephanandra: 2 species) was carried out using scanning electron microscopy in order to evaluate the taxonomic and systematic implications of these characteristics. The leaves of the genera Neillia and Stephanandra were hypostomatic, whereas those of P. monogynus, P. opulifolius were amphistomatic. The range of the size of the stomata is $12.02-34.39{\times}10.76-27.13{\mu}m$; the smallest was found in N. thyrsiflora (average $13.98{\times}12.43{\mu}m$; $L{\times}W$), while the largest was measured in N. gracilis (average $26.82{\times}20.67{\mu}m$; $L{\times}W$). Paracytic stomata complexes are only found in N. affinis, and the anomocytic type was most commonly found. The papillate epidermal cell type was only observed on the abaxial surfaces of P. insularis. Platelet epicuticular waxes were found on the adaxial surfaces of N. affinis and S. tanakae. Four types (unicellular non-glandular, two- to five-armed, stellate, and glandular) of trichomes were found on the leaves. Stellates were observed in all species of Physocarpus except for P. insularis. Consequently, leaf epidermal micromorphological characteristics (e.g., the presence of papillate epidermal cells and stellate, and stomata complexes) may have high taxonomic and systematic value in Neillieae. Our results strongly support previous molecular phylogenetic and palynological hypotheses that Stephanandra and Neillia are a single genus and that Physocarpus insularis should be considered as a member of Spiraea.

• Korean Journal of Plant Resources
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• v.29 no.5
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• pp.555-563
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• 2016

The morphological characteristics and genetic relationships among 32 germplasms of Zanthoxylum schinifolium and Zanthoxylum piperitum collected from two farms in Korea were investigated. The traits with the most variability were seed color, leaf size, and spine size. The intraspecific polymorphism of Z. schinifolium and Z. piperitum was 96.5% and 60.3%, respectively. The genetic diversity and Shannon’s information index values ranged from 0.11 to 0.33 and 0.19 to 0.50, with average values of 0.26 and 0.42, respectively. Two ISSR primers (UBC861 and UBC862) were able to distinguish the different species. The genetic similarity matrix (GSM) revealed variability among the accessions ranging from 0.116 to 0.816. The intraspecific GSM for Z. schinifolium and Z. piperitum was 0.177-0.780 and 0.250-0.816, respectively. The GSM findings indicate that Z. schinifolium and Z. piperitum accessions have high genetic diversity and possess germplasms qualifying as good genetic resources for cross breeding. The clustering analysis separated Z. schinifolium and Z. piperitum into independent groups, and all accessions could be classified into three categories. Z. Schinifolium var. nermis belonged to independent groups. Comparison of the clusters based on morphological analysis with those based on ISSR data resulted in an unclear pattern of division among the accessions. The study findings indicate that Z. schinifolium and Z. piperitum accessions have genetic diversity, and ISSR markers were useful for identifying Z. schinifolium and Z. piperitum.

• Korean Journal of Plant Taxonomy
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• v.34 no.3
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• pp.189-203
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• 2004

Numerical analysis based on 33 morphological characters from 25 populations of 8 species of tribe Forsythieae in Korea was conducted to investigate the taxonomic delimitation and discuss the systematic relationships. In this study, Fontanesia phyllyreoides Labill was adopted as comparing outgroup to discuss the taxonomic status of Abeliophyllum distichum and elucidate the taxonomic relationships between tribe Forsythieae and tribe Fontanesiae. Based on the results of PCA, the sum of contributions for the total variance of three major principal components was 79.6% (PC1 54.2%, PC2 15.4% and PC3 10.0%, repectively). Two dimensional plotting from PCA results recognized three distinct generic clusters. Among the populations of Forsythia, two distinct groups were clustered as I. koreana-saxatilis-viridissima and II. ovata-nakaii. However, 15 populations of Abeliophyllum distichum were arranged randomly without any tendency, and the infraspecies of Abeliophyllum distichum could be recognized as individual variations. Fontanesia phyllyreoides Labill was clustered independently and intertribal limitation was clearly distinguished.

• Korean Journal of Plant Taxonomy
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• v.46 no.1
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• pp.13-32
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• 2016

Neillieae was traditionally recognized as a small tribe in Rosaceae, which consists of Neillia, Stephanandra, and Physocarpus. Recently, Stephanandra was merged into Neillia based on molecular phylogenetic analyses, meaning that Neillieae now contains Neillia and Physocarpus. The genus Neillia is distinguished from Physocarpus by ovate to lanceolate leaves with acuminate to caudate apices, racemose or paniculate inflorescences, and a unicarpellate (rarely bicarpellate) gynoecium. Plants of Neillia are distributed from the Himalayas across China and Korea to Japan in the east, and south to Indonesia. This study provides a taxonomic treatment of Neillia based on a morphological examination of herbarium specimens, including types, and field observations, as the second part of the taxonomic revision of the tribe Neillieae. A summary of the phylogeny of Neillia, keys to the species, nomenclatural reviews, descriptions, distribution maps, and lists of specimens examined are provided. Twelve species with ten varieties are recognized in Neillia. A lectotype was designated here for the following species: N. sinensis f. glanduligera and N. thyrsiflora.

• The Korean Journal of Zoology
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• v.37 no.2
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• pp.213-221
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• 1994

한국산 산호충류의 계통분류학적 연구의 일환으로 1969년부터 1986년까지 우리나라의 삼면 연안과 도서 지방으로부터 채집된 돌산호류 중 대한해협의 미포에서 그물에 의해 채집된 나무돌산호 과의 1종이 신속, 신종으로 밝혀져 미립이분지돌산호(dichopsammia granulosa)라고 명명하고 기재한다. 이들의 완모식 표본과 대부분의 부모식 표본들은 이화여자대학교 자연과학대학 생물과학과에 보관되어 있고, 일부 부모식 표본은 이화여자대학교 자연사박물관에 보관되어 있다.