NGS data was yielded by using Illumina Hiseq platform. The short reads were filtered by quality score and read length were mapped against the reference genome (KACC42780). Genome-wide reanalyzed data of Flammulina strains were compared against the reference genome to establish a genome-wide single nucleotide polymorphism (SNP). The rate of mapping differences between the strains reflected in the strain variation in its result. The genome-wide SNPs distribution divided into types of homozygous SNP and heterozygous SNP moreover all of the strains demonstrated a wide variation in all of the regions. In the further study of topological relationship between the collected strains, phylogenetic tree was separated into 3 major groups. Group I contained F. velutipes var. related strains of ASI 4062, 4148, 4195. Group Ⅱ contained strains that were different species of ASI 4188 F. elastica, ASI 4190 F. fennae, and ASI 4194 F. rossica. The other 19 strains F. velutipes were classified as a single group. Polymorphic SNPs of F. velutipes strains representing the phylogenetic segregation of whiteand brown-fruiting body forming groups were compared. As previously reported, white gene expression is recessive to brown in fruiting body color gene expression. The white strains produced 131,874 SNPs to be aa type and homozygous from of SNP. 407,947 SNPs were detected as AA, Aa type from the brown-fruiting body of SNP. We constructed a SNP matrix with 8 white strains and 12 brown strains. To develop the molecular marker related in to fruiting body color and geographical origin, we isolated 240 SNPs from the white-and brown-fruiting body forming. To determine the chromosome relationship on polymorphic SNP between Korea and Japan strains producing white-fruiting body, we analyzed that the Korea white strains detected 185,695 SNPs and the Japan white strains produced 263,811 SNPs. Using the constructed SNP matrix with 3 Korea white strains and 3 Japan white strains, the experiment generated 475 SNPs of phylogenetic SNPs fromKorea and Japan white-fruiting body. As a result, we regarded as they are potentially related to the white color. White and brown color and origin specific SNPs could be used as an identification marker for selection of F. veluipes strains in the breeding program.

This study was carried out to investigate the bat (Chiroptera) fauna in Jeju Island. Bat distribution has been monitored for last eleven years (since July 2006 to April 2016). We visited and survey the bat distribution in fifteen natural lava tubes, three sea caves, nineteen artificial cave encampments constructed during 20th century, five natural forest regions nearby Hallasan (eco-corridors) and one sea-shore area. Bat specimens were also confirmed at two local museums in Jeju Island. From the present study, we found 9 species of 6 genera belong to 3 families, which was quitely different from the records had previously described in Jeju Island since 1928. Five species (Rhinolophus ferrumequium, Myotis bombinus, Myotis rufoniger, Myotis macrodactylus and Miniopterus schreibersi) were commonly found to live in lava tubes and cave enforcements. But only Rhinolophus ferrumequium was found in a sea cave and five species including Murina leucogaster and Pipistrellus abramus were found in eco-corridors. Myotis aurascens were only observed in the cave enforcements. We have also confirmed the existence of specimens, including Tadarida insignis, stored at the local museums. From the results of this study, we actually could not found the remaining seven species (Hypsugo savii, Miniopterus fuscus, Myotis mystacinus, Myotis ikonnikovi, Myotis branditii, Myotis petax and Pipistrellus endoi). From the investigation of bat species, Myotis rufoniger which is known as one of endangered species were detected in four different locations including two lava tubes, one forest region, and one cave enforcement. This is the first time of finding for Myotis rufoniger in the artificial architecture. In addition, one of rare finding species Myotis bombinus in Korean Peninsula, which were found in several lava tubes and cave enforcements, in some cases they were observed in the large population over one-hundred individuals. The Tube-nosed bat (Murina leucogaster) was discovered for the first time through this study in 2009, which was found in the mountainous forest regions nearby Hallasan in summer season. Interestingly, Myotis aurascens were also discovered firstly in spring season of 2015. Myotis aurascens were discovered three locations of cave enforcements but the localities were restricted only in the western region of Jeju Island. Using the bat specimens fo Myotis aurascens collected from three different locations, we tried to examine the morphometric and phylogenetic relationship among the records in the East Asia. The bat population of Jeju Island had smaller levels of HBL and Hfcu, but greater levels of TL, EL, FAL, and Tra than those of the Korean Peninsula population. Jeju bats had wide range in the lengths of FAL and Hfcu comparing to those of European bats. From the bimonthly monitoring to each finding site, we have actually failed to observe those again, estimating that they use those CEs as the daily-roosting place in activating seasons. The sequences of CYTB and COI genes showed identical sequences among Jeju Myotis aurascens bats tested, indicating that they are maternally related. The results from molecular phylogeny showed that the sequences of these bats located on the same branch with those for Myotis aurascens in the phylogenetic trees. Besides, the nucleotide sequences of the Jeju Myotis aurascens bats showed the closest relation with those of Korean Peninsula. Consequently, these findings indicate that the bats of Myotis aurascens, verified the natural distribution in Jeju Island, have originated from a single maternal origin and differences in morphological and genetic backgrounds form those of Korean Peninsula and the other countries, and had probably immigrated via Korean Peninsula from the northwest. The results of this study showed that it should be carried out to reconstruct the bat fauna and to reveal the natural habitation status of each species in this island in the future. In addition, these findings will contribute as basic information for understanding the migration history and biogeographic relationship of bats in East Asia, and for planning the conservation and management programs of the wildlife in Jeju Island.

동절기에 제주도 지역에서 도래하는 떼까마귀의 유전적 특성과 집단 간 유연관계를 구명하기 위해, 미토콘드리아 COI 유전자 서열의 다형성에 기반한 모계 계통 구조와 계통 유연관계를 분석하였다. 떼까마귀 DNA는 우도와 제주도 내에서 발견된 깃털과 사체 시료에서 분리하였다. 결정된 COI 서열들(n=41)은 떼까마귀(Corvus frugilegus)에서 기존 에 보고된 서열들과 97.0% 이상 일치하였다. 제주도 떼까마귀 COI 서열들은 3가지 haplotype(J01-J03)으로 구분되었으 나 지역-특이적인 양상을 보이지 않아, 이들이 하나의 모계 기원에서 유래한 집단임을 알 수 있었다. 떼까마귀 전체 COI 서열에서 8개의 COI haplotype들이 발견되었다. 이 중 3가지 haplotype들은 러시아 동부, 몽골, 한국 등 동북아시 아의 COI 서열들을 포함하였고, 나머지 5가지는 중앙아시아, 중동아시아, 러시아 서부, 유럽국가의 떼까마귀에서 발견 되었다. 계통수 상에서 떼까마귀의 COI 서열들은 측소적 종분화 단계인 2아종, C. f. frugilegus와 C. f. pastinator인 2개의 모계 계통으로 뚜렷하게 구분되었다. DNA barcoding 분석을 통한 연구결과는 모계 계통의 구조, 계통 유연관계 및 분자생태를 이해하는 데 중요한 정보를 제공할 것이다.

Cordyceps bassiana (asexual stage Beauveriabassiana) is a widely distributed entomopathogenic fungus that infects hundreds of various insects. It produces a number of secondary metabolites, including insect toxins beauvericin and bassianolide and pigment tenellin. In the present study, members of NRPS and PKS-NRPS hybrid genes were predicted from whole genome sequences of eighteen different fungal species belonging to five families of Hypocreales (Cordycipitaceae, Clavicipitaceae, Ophiocordycipitaceae, Hypocreaceae and Nectriaceae) using antiSMASH ver. 1.2.2. Phylogeny using all predicted adenylation (A) domains was drawn in order to identify potential orthologous genes of beauvericin synthetase (BbBEAS) and bassianolide synthetase (BbBSLS) in Hypocreales. The orthologs were examined to understand the evolution of beauvericin and bassianolide synthetase genes. Phylogenetic tree shows grouping of A1 and A2 domains of BbBEAS, BbBSLS and enniatin synthetases in two separate clades indicating the origin of genes from fusion of two distantly related modules. Species phylogeny of C. bassiana and its allies is congruent with gene trees of BbBEAS and BbBSLS, suggesting that the gene fusion event predates the species divergence. In the inferred phylogeny, A1 domain of BbBEAS showed highest similarity with that of BbBSLS, followed by those of Fusarium equiseti enniatin synthetase and Xylariasp. bassianolide synthetase. Syntenic analysis of beauvericin gene clusters of C. bassiana and closely related species represents that C. militaris lost the BbBEAS gene in evolution. Synteny of bassianolide gene clusters shows the loss of NRPS genes encoding BbBSLS in B. pseudobassiana, Isaria tenuipes, I. farinosa and C. pruinosa. BbBEAS and 2-ketoisovalerate reductase (kivr) genes are found conserved in beauvericin and enniatin synthesizing gene clusters.

In Korea, twelve species in genus Myrmica have been described. Some of them are morphologically similar and this makes their identification difficult. For this reason, we collected several Myrmica species in question and inferred their phylogenetic relationship using the 418bp partial COI (cytochrome C oxidase 1) region from a total of 33 individuals. We found that the CO1 haplotypes are effectively grouped into three clusters that match well to their external morphological characters. Although this three species could be distinguished by the only small part of the COI region, the two individual sample of the M. kotokuii and one sample of the M. carinata are included in the M. kurokii group. The results indicate that the morphological identification could be obscure in the three species and it requires a close examination for this phenomenon.

Uroleucon is one of the large aphid genera including some important pest on agricultural crops, mostly feeding on Asteraceae, few species on Campanulaceae. In this study, we suggest the phylogenetic position of Uroleucon in the tribe Macrosiphini, and subgeneric relationship of the main three subgenera using mitochondrial and nuclear genes: tRNA-leucine+cytochrome oxidaseⅡ(tRNA+COII) and Elongation factor-1 alpha gene (EF1α)). With the results of comprehensive molecular phylogenetic study by Bayesian phylogeny (BP) and Maximum-likelihood (ML) using combined data sets of two molecular markers, we reconstruct subgeneric relationship with the data of host plants and morphological characters.

The cladistics analysis of subfamily Phylinae, based on molecular data analysis of 3655 base pairs of mitochondrial (16S, COI) and nuclear (18S, 28S) ribosomal DNA for 66 taxa in five tribes were conducted. Partitions of datasets were aligned using different algorithms implemented in MAFFT, further combined through sequence matrix and the combined dataset was analyzed using partitioned maximum likelihood. Clades in analytical method comprise six subfamilies of Miridae as outgroup: Isometopinae, Cylapinae, Bryocorinae, Orthotylinae, Deraeocorinae, and Mirinae, and five tribes of ingroup in subfamily Phylinae: Auricillocorini, Hallodapini, Phylini, Leucophoropterini, and Pilophorini. In analysis, tribe Auricillocorini as sister group to all remaining phylines. Most of the tribes are monophyly, except largest tribe phylini, which is clearly divided as paraphyly.

Halacarid mites inhabit mainly in the bottom of the sea and their body lengths are approximately 0.5 mm. Few biological information about halacarids have been obtained. The phylogenetic study of halacarid mites has not been progressed and the phylogenetic relationship within the family Halacaridae is still unknown. Particularly there is no molecular study to infer phylogenetic relationship within the family. In the annual meeting of Acarological Society of Japan 2007, we developed the method for molecular analysis of 28S nuclear ribosomal gene in haracarid mites. Subsequently, we have further progressed the technique of the molecular analysis to infer the phylogenetic relationship of haracarids. The aim of the present study is to elucidate the phylogenetic position of the subfamily Rhombognathinae on the bases of molecular data. Halacarid specimens which were obtained from seaweeds and sandy segment at Japanese seacoasts, consist of eight genera in five subfamilies: Halacarinae (Halacarus sp., Agauopsis spp., Thalassarachna spp.), Halixodinae (Badyagaue sp., Agaue sp.), Copidgnathinae (Copidognathus spp.), Actacarinae (Actacarus spp.) and Rhombognathinae (Rhombognathus spp.). The template DNA was extracted and 28S nuclear ribosomal gene of the DNA was amplified by PCR reactions. And we determined approximately 400 base pair length of the gene. To construct phylogenetic trees by neighbor-joining method we calculated genetic distances of each operational taxonomic unit considering 1) transversions and 2) transitions and transversions based on Tamura - Nei model by using MEGA ver. 4 (Tamura et al. 2007). As a result, we got two trees both showing two main clusters. One of them includes only one subfamily Rhombognathinae and another consist of Halacarinae, Copidgnathnae, Actacarinae and Halixodinae. Rhombognathinae was greatly differentiated from the other subfamilies. Thus, Rhombognathinae possibly is a distinct taxon phylogenetically and this result supports the monophyletic nature obtained previously by morphological analysis.

Dysphania ambrosioides (L.) Mosyakin & Clemants which belongs to Chenopodiaceae/Amaranthaceae sensu in APG system has been known as a useful plant in various fields as well as an invasive species spreading all over the world. To understand its phylogenetic relationship with neighbour species, we completed chloroplast genome of D. ambrosioides collected in Korea. Its length is 151,689 bp consisting of four sub-regions: 83,421 bp of large single copy (LSC) and 18,062 bp of small single copy (SSC) regions are separated by 25,103 bp of inverted repeat (IR) regions. 128 genes (84 protein-coding genes, eight rRNAs, and 36 tRNAs) were annotated. The overall GC content of the chloroplast genome is 36.9% and those in the LSC, SSC and IR regions are 34.9%, 30.3%, and 42.7%, respectively. Distribution of simple sequence repeats are similar to those of the other two Dysphania chloroplasts; however, different features can be utilized for population genetics. Nucleotide diversity of Dysphania chloroplast genomes 18 genes including two ribosomal RNAs contains high nucleotide diversity peaks, which may be genus or species-specific manner. Phylogenetic tree presents that D. ambrosioides occupied a basal position in genus Dysphania and phylogenetic relation of tribe level is presented clearly with complete chloroplast genomes.

다양한 환경에서 수집한 국내 민들레속 유전자원 수집종의 엽록체 DNA 영역(trnL-trnF와 rps16-trnK) 염기서열을 이용하여 종내․ 간 변이 및 배수성을 구명하여 유전자원 육성의 기초 자료룰 제공하고자 수행하였다. 민들레속 유전자원의 배수성은 털민들레, 서양민들레, 붉은씨서양민들레가 3배체이고, 흰 민들레와 흰노랑민들레는 4배체였다. 염기서열의 길이는 trnLtrnF 영역에서 자생종류인 털민들레, 흰민들레, 흰노랑민들레 가 931 bp에서 935 bp, 서양민들레는 910 bp, 붉은씨서양민들레 는 975 bp로 종간 차이를 나타내었고, 종 특이적 염기서열 88개, 자생종 및 귀화종 특이적 염기서열 41개가 검출되었다. rps16- trnK 영역은 털민들레 882∼883 bp, 흰민들레 875∼881 bp, 흰 노랑민들레는 878∼883 bp 서양민들레 874∼876 bp, 붉은씨서 양민들레는 847∼848 bp로 37개 종특이적 염기서열이 검출되 었다. 염기서열의 유사도는 trnL-trnF 영역에서 0.860∼1.000 사이로 평균 0.949이며, rps16-trnK 영역의 유사도는 0.919∼ 1.000 사이로 평균 0.967이었다. 염기서열을 바탕으로 유연관계를 분석한 결과, trnL-trnF 영역은 크게 자생종류와 귀화종 류로 구분되었으며, 서양민들레와 붉은씨서양민들레는 같은 종 간에 유집되었고, 자생종류는 분리되지 않았으며, rps16-trnK 4개 그룹과 유집되지 않은 5개체로 나뉘었다. 흰노랑민들레는 두 영역 모두 흰민들레와 동일 계통군을 형성하였고, 염기서열 상 두 종간 뚜렷한 차이가 없었다. 유연관계에서 모두 독립적으로 존재한 흰민들레 No. 10 (조계산)과 털민들레 1번(광양)은 민들레 유전자원 육성소재로 활용이 기대된다.

The 12 cultivars of the Jeju native Citrus are considered to have originated from China. However, the origin of the cultivar ‘Byungkyool’ (Citrus platymamma Hort. ex Tanaka) is not clearly known. We performed PCR analysis by using three primer sets designed from the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) to analyze the phylogenetic relationship between the traditional citrus cultivars and the Byungkyool cultivar. Sequence length of the nrDNA ITS1 region of JNCPCRI (Jeju Native Citrus platymamma Citrus Research Institute) cultivar was 247 bp, 8the ITS2 region was 228 bp and the total ITS region (ITS1-5.8S-ITS2) was 638 bp. Analysis of the genetic relationship based on the sequence analysis at the ITS region of the JNCPCRI cultivar revealed that the ITS1 region of the cultivar was genetically the same as that of the Byungkyool (JQ990189) cultivar, and the ITS2 region was genetically similar to the Binkyool (JQ990180), Hongkyool (JQ990178), Dangyooja (JQ990179), and Pyunkyool (JQ990181) cultivars. Moreover, the total ITS region in the 5.8S rDNA region was genetically similar to the Hongkyool (JQ990178) cultivar. In addition, the total ITS region of the JNCPCRI cultivar was the most closely related to the Cheongkyool (JQ990183) cultivar and has been reported to originate from the Binkyool (JQ990180) and Pyunkyool (JQ990181) cultivars. Although the JNCPCRI cultivar was morphologically the same as the Byungkyool (JQ990189) cultivar, the ITS region showed genetic heterogeneity. Taken together, we conclude that the genetic variation in the ITS region of JNCPCRI cultivar suggests that it was propagated through fertilization with the surrounding citrus cultivars.

Angelica gigas, also called Dang Gui or Korean Angelica, is a major medicinal herb used in Asian countries such as Korea, Japan and China. In Korea, we are using the roots of A. gigas., but, they are using Angelica sinensis in China and using Angelica acutiloba. in Japan to obtain many active constituents such as dercursin, decursinol angelate, nodakenetin, nodakenin, umbelliferone, β-sisterol, or α-pinene. The plants of the Angelica family are used to improve gynecological health. The biggest problem in the cultivation of A. gigas is bolting. If the bolting occurs, A. gigas can not be used as a medicinal component because the roots are lignified. In this study, 11 A. gigas genetic resources in Korea; 1. Hwangje variety, 2. Sungwoo Jongmyo company, 3. Bonghwa No. 1, 4. Bonghwa No. 2, 5. Bonghwa No. 3, 6. Bonghwa No. 4, 7. Jechun local variety, 8. Jirisan local variety, 9. Manchu variety in Eumseong, 10. Manchu variety in Bonghwa, 11. Jinbu local variety, were collected and performed phylogenetic analysis using RAPD molecular markers.

Adenophora triphylla var. japonica HARA is a herbaceous plant belongs to Campanulaceae. Adenophora root is mainly used for medicinal purpose. It is effective for lung cleaning, sputum remove, viscera strengthening, cough stopping and cancer treatments. Adenophora has about 70 species in the world and 17 of the species are distributed in Korea. Genetic resources of A. triphylla var. japonica HARA are valuable as the habitat is concentrated in East Asia. The intraspecies variation is very high according to the environmental conditions. A new A. triphylla var. japonica HARA variety, ‘Harang’, was developed through polyploid breeding in 2011. But, low domestic production and passive studies caused our country to rely on imports for almost all amount of the A. triphylla var. japonica HARA demands. In this experiment, genetic diversity between the collections were analyzed using 32 RAPD primers. Through this study, limit of morphologic classification could be solved and genetic diversity of this plant could be assured.

Codonopsis lanceolata is used as a natural medicine or vegetables. It originates in East Asia such as Korea, Japan and China. Similar to Panax ginseng, C. lanceolata contains saponins as effective components. C. lanceolata is cultivated in many regions of South Korea. But, no variety was developed yet and the origin discrimination in the distribution market of C. lanceolata became a problem. In this study, we collected 20 C. lanceolata regional groups; Hoengseong, Wonju, Samcheok, Chuncheon, Pyeongchang, Hongcheon, Yongin, Yangpyeong, Danyang, Chungju, Bonghwa, Ulleung, Yeongju, Sancheong, Muju, Gwangyang, Sinan, Hwasun, Jeju-si and Seogwipo-si, and tested the genetic relationship using RAPD molecular markers. The genomic DNA was extracted using CTAB and the RAPD analysis was performed using 32 primers of Operon Technologies. NTsys-PC program was used for the phylogenetic analysis of the data.

Platycodon grandiflorum is a perennial herbal plant belongs to Campanulaceae family. It has very important genetic value as a major plant in Asterids order. The major ingredients are platycosides, terpenoid saponins. In Korean industrial plants market, it was produced 5,633 tons in 2013, and the total amount of production was less than only five species, omija, ginger, raspberry, yam and deodeok. P. grandiflorum is called ‘Gilgyung’ and is used as a fresh vegetable and an ornamental plant. Nowadays, various components of P. grandiflorum were already published. But, genetic research is in the starting stage. In this study, 11 cultivars; 1. MariesⅡ, 2. Hakone double white, 3. Hakone double blue, 4. Fuji white, 5. Fuji pink, 6. Fuji blue, 7. Astra white, 8. Astra pink, 9. Astra blue, 10. Astrasemi double blue, 11. Jangback, were analyzed using 60 Operon Universal RAPD primers. The results were phylogenetically analyzed and related to the morphological characteristics of the cultivars.