Internal transcribed spacer-based CAPS marker development for <i>Lilium hansonii</i> identification from wild <i>Lilium</i> native to Korea

Kumari, Shipra,Kanth, Bashistha Kumar,Jeon, Yongsam,Jang, Ji-Young,Kim, Hyun-Soon,Lee, Geung-Joo Elsevier 2018 Scientia horticulturae Vol.236 No.-

<P>We have developed a cleaved amplified polymorphic sequence (CAPS) marker with the aim of identifying the best species among the different wild Lilium species native to Korea for breeding purpose. The CAPS marker is based on single nucleotide polymorphisms (SNPs) in the nucleotide sequences of the internal transcribed spacer genes, which are widely used in the breeding of angiosperms. We cloned and sequenced the ITS regions of nuclear ribosomal genes from 11 Lilium species and deduced the phylogenetic relationships among them. Phylogenetic analysis based on the maximum likelihood method showed that Lilium species formed a monophyletic Glade and were divided into two groups that linked to the two sections, Martagon and Sinomartagon, out of seven sections of Lilium. The lengths of the ITS1 and ITS2 regions in the wild native Lilium species were distinct, and nucleotide polymorphisms were distinguished in these regions. A conserved region in the sequence was found from position 330-340 in all the species. We analyzed the SNP sites and found a suitable restriction endonuclease, Eco52I, having six base pair recognition site, to be suitable for the development of the CAPS marker. Among the 11 Lilium species, only the amplicon from the ITS region of L. hansonii contained the restriction site and produced two distinct bands of around 623 and 268 bp upon digestion with Eco52I. The genotyping of the 11 wild Lilium species by the developed marker can be recommended for breeding programs as it provides an indirect selection of plants and can effectively differentiate wild native lilies. The method using CAPS marker is simple, quick, and highly reliable for identifying the best species for efficient breeding of Lilium.</P>

한라산 고유 한라송이풀의 분류학적 위치

조원범,최병희 한국식물분류학회 2011 식물 분류학회지 Vol.41 No.2

Pedicularis growing at Mt. Halla of Jeju Island is known as an endemic species of P. hallaisanensis Hurusawa. On the other hand, the plant is morphologically similar to P. amoena, P. spicata, and P. verticillata in gross morphology, so the taxonomic treatment of the taxon remains controversial. To clarify the taxonomic position of the plants, we examined external morphological characters and nuclear ribosomal DNA ITS sequences for P. hallaisanensis and its related species. The plants of Mt. Halla are clearly different from P. amoena and P. verticillata in the morphology of calyx lobes, the length of galea and lower lip, density of glandular hairs on plants, presences of the radical leaves after anthesis and molecular data. However, P. hallaisanensis is not clearly separated from P. spicata distributed in N. E. Asia on external morphological characters and DNA sequences of internal transcribed spacers. In this study, the morphological and molecular data suggested that P. hallaisanensis should be merged into the former species. 제주도 한라산에 자라는 한라송이풀은 고유종 Pedicularis hallaisanensis Hurusawa로 인식되고 있다. 한편 이 식물은 근연종인 P. amoena, 구름송이풀 또는 이삭송이풀과 형태적으로 유사하여 분류학적 처리가 혼동되어왔다. 본 연구는 이 식물의 분류학적 위치를 파악하기 위하여 한라송이풀과 근연종을 대상으로 외부형태 및 핵 리보소옴 DNA 염기서열을 조사하였다. 한라산의 이 식물은 꽃받침 열편, 화판 상순과 하순의 길이 비, 식물체의 선모 밀도, 개화기 근생엽의 유무 및 염기서열 자료에서 P. amoena 및 구름송이풀과는 뚜렷한 차이를 보였다. 하지만 한라송이풀은 외부형태 및 ITS 염기서열에서 동북아에 분포하는 이삭송이풀과 뚜렷이 구별되지 않았다. 본 연구의 형태 및 분자생물학적 자료는 한라송이풀이 이삭송이풀로 통합되는 것을 지지하였다.

Intraspecific Hybridization of Anopheles sinensis (Diptera: Culicidae) Strains from Thailand and Korea

민기식,Wej Choochote,Atchariya Jitpakdi,김세주,김원,정종우,Anuluck Junkum 한국분자세포생물학회 2002 Molecules and cells Vol.14 No.2

Anopheles (Anopheles) sinensis [Wiedemann (1828)] is a member of the hyrcanus species group, and it has been incriminated as the natural or experimental ma-laria vectors in the Republic of Korea, Japan, China, and Indonesia. In Thailand, however, An. sinensis seems to be of little medical importance. Hybridization tests among the three iso-female lines (isolines) of An. sinensis [i.e., Form A (X, Y1) and Form B (X, Y2) (Thailand strain), and Form B (X, Y2) (Korean strain)] were established based on two distinct types of meta-phase chromosomes and geographical differences. The chromosomal form of the Korean strain was first iden-tified from this study. Results of reciprocal and back crosses indicated that both karyotypic forms of the An. sinensis Thailand and Korean strains were genetically compatible, and provided viable progenies and com-pletely synaptic polytene chromosomes. The sequences of the rDNA internal-transcribed spacer 2 (ITS2) and mitochondrial cytochrome c oxidase subunit II (COII) among the An. sinensis strains were nearly identical to each other, and the intraspecific sequence variability was very low (0.0-0.6%). Sequence comparisons among the cryptic inter-species (i.e., An. sinensis, An. lesteri, and An. yatsushiroensis), however, revealed ex-tensive divergence, and the intraspecific variability ranged from 12.2 to 34.6%. Therefore, it is concluded from these results and previous vector ability studies that the An. sinensis Forms A and B exhibit cytological polymorphic races that have different vector abilities in their transmission of malaria, depending on their geo-graphical locations.

Two New Species of Cryptococcus sp. and Candida sp. from Wild Flowers in Korea

( Jin Hong Min ),( Min Gu Kang ),( Jin Ju Ryu ),( Hyang Burm Lee ),( Chang Mu Kim ),( Ha Kun Kim ),( Jong Soo Lee ) 한국균학회 2012 Mycobiology Vol.40 No.4

Among 80 types of yeast isolated from wild flowers in Daejeon, Korea, two species that have not yet been identified by phylogenetic analysis of the internal transcribed spacer-2 (ITS2) genes and 26S rDNA sequences were identified as Candida sp. 44-C-1 and Cryptococcus sp. 9-D-1. Neither of the newly identified species formed ascospores, while Candida sp. 44-C- 1 formed pseudomycelium and Cryptococcus sp. 9-D-1 did not.

애완동물로부터 감염된 환자 및 애완동물에서 분리된 T. mentagrophytes 의 internal transcribed spacer 1 ( ITS1 ) 염기서열 분석

김정애(Jeong Aee Kim),임종현(Jong Hyun Rim),문상은(Sang Eun Moon),김규한(Kyu Han Kim),조광현(Kwang Hyun Cho) 대한피부과학회 2001 대한피부과학회지 Vol.39 No.10

N/A Background: Trichophyton mentagrophytes is a complex species and 3 perfect states, Arthroderma benhamiae, A. vanbreuseghemii, and A. simii have been described. In Korea and Japan, all of the isolates of T. mentagrophytes of which the perfect states determined were known as A. vanbreuseghemii till recently. However, in Japan, one isolate from a monkey was reported as A. simii and several strains from rabbits or patients were A. benhamiae. Therefore, it is necessary to confirm the existence of A. simii or A. benhamiae in Korea. Objectives: We performed this study to determine the teleomorphs of 19 strains of T. mentagrophytes isolated from Korean patients infected from pets and 4 from the skin lesions of rabbits. Metbods: DNA sequences of internal transcribed spacer 1 (ITS1) area of the 23 isolates and 3 reference strains were determined and matched with the data registered in GenBank nucleotide sequence database. Results: The sequencing data of 22 isolates were very similar to those of A. vanbreuseghemii and 1 to T, mentagrophytes var. interdigitale respectively. Conclusion '. Although all of the clinical isolates were related with A. vanbreuseghemii in this study, the possibility of the existence of A. simii and A. benhamiae in Korea is still high and further study is needed. (Korean J Dermatol 2001;39(8): 1086-1093)

Internal transcribed spacer (ITS) region의 염기서열 분석에 의한 보길도산 황칠나무의 분자 계통학적 연구

신용국(Yong Kook Shin) 한국생명과학회 2016 생명과학회지 Vol.26 No.11

보길도에서 자라고 있는 황칠나무(Dendropanax morbifera)를 구입하여, 캘러스로 유도한 후, ribosomal DNA(nrDNA)의 internal transcribed spacer (ITS) region의 염기서열을 결정하였다 보길도의 황칠나무(Dendropanax morbifera)의 ITS region의 염기서열을 분석한 결과, 총 689염기를 결정하였다. 결정된 689염기 중에서 ITS1은 222개염기, 5.8S rDNA는 160염기, ITS2는 233염기인 것으로 판명되었다. GenBank의 BLAST 프로그램(http://www. ncbi.nlm.nih.BLAST)을 사용하여 GenBank/EMBL/DDBJ에 등록되어 있는 Dendropanax 속 33의 염기서열을 수집한 후 multiple alignment를 수행한 결과, 유사도는 99.7%(D. chevalieri)에서 92.6%(Dendropanax arboreus)로 나타났으며, 일본황칠나무(D. trifidus)와는 유사도가 99.4%로 판명되었다. Dendropanax morbifera is an endemic tree species of Korea, it is restricted to the southern parts of Korea. The internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) for Dendropanax morbifera grown at Bogil-do, Korea was determined. We investigated the sequence-based phylogenetic relationships of plants related and clarified its taxonomical position. The determined sequences consisted of 689 residues. ITS1 was 222 bp long while ITS2 was 233 bp long. The 5.8S rDNA was 160 bp long. The ITS region sequences of the Dendropanax species included in this study were obtained from GenBank. Oreopanax polycephalus was used as the outgroup. A pairwise alignment was calculated using the Clustal X program. A phylogenetic tree was constructed by the neighbor-joining method using the Tree view program. Sequence similarities among species including D. morbifera Bogil-do isolate showed the range 92.6 to 99.7% in sequence-based phylogenetic analysis using total 615 base pairs of ITS1, 5.8S rDNA and ITS2. D. morbifera Bogil-do isolate exhibited the highest degree of relatedness to D. chevalieri, sharing 99.7% ITS region similarity. D. morbifera Bogil-do isolate also showed to D. trifidus, sharing 99.4% ITS region similarity.

Molecular Phylogeny of Silk Producing Insects Based on Internal Transcribed Spacer DNA1

Mahendran, Botlagunta,Ghosh, Sudip K.,Kundu, Subhas C. Korean Society for Biochemistry and Molecular Biol 2006 Journal of biochemistry and molecular biology Vol.39 No.5

Silk moths are the best studied silk secreting insects and belong to the families Bombycidae and Saturniidae. The phylogenetic relationship between eleven silk producing insects was analyzed using the complete DNA sequence of the internal transcribed spacer DNA 1 locus. The PCR amplification and sequence analysis showed variation in length ranging from 138 bp (Antheraea polyphemus) to 911 bp (Hyalopora cecropia). Microsatellite sequences were found and was be used to distinguish Saturniidae and Bombycidae members. The nucleotide sequences were aligned manually and used for construction of phylogenetic trees based on Maximum parsimony and Maximum likelihood methods. The topology in both the approaches yielded a similar tree that supports the ancestral position of the Antheraea assama.

Internal Transcribed Spacers (ITS)로 분석한 국내 Rubus 재배종의 계통학적 유연관계

유기석,박명렬,윤성중 韓國藥用作物學會 2009 한국약용작물학회지 Vol.17 No.3

The bramble cultivated widely in South Korea, which is known as Bokbunja-ddal-gi, is regarded as having originated from Korean native Rubus coreanus. This study was carried out to obtain basic phylogenetic information on Korean cultivated bramble (KCB) by comparing the internal transcribed spacer (ITS) regions with those of R. coreanus, blackberry (R. lanciniatus), black (R. occidentalis) and red (R. idaeus) raspberry. Sequences of the ITS 1 suggest that some KCB accessions share a significant similarity with both R. occidentalis and R. coreanus in the ITS 1 region. The ITS 2 sequences of the three KCB accessions clustered more closely to those of two R. occidentalis accessions than to those of R. coreanus. These results suggest that there exist variations in the sequences of ITS among KCB accessions and KCB accessions are more closely related to black raspberry than R. coreanus in the ITS regions.

Molecular Phylogeny of Silk Producing Insects Based on Internal Transcribed Spacer DNA1

( Botlagunta Mahendran ),( Sudip K. Ghosh ),( Subhas C. Kundu ) 생화학분자생물학회 2006 BMB Reports Vol.39 No.5

DNA 바코드 분석을 통한 개자 및 운대자 감별

노푸름,여상민,김욱진,양선규,박인규,문병철 한국원예학회 2018 원예과학기술지 Vol.36 No.6

Brassica juncea and Brassica napus are economically important crops used for oilseed and foragewho’s seed is also used for herbal medicines, namely Brassicae Semen and Brassicae CampestrisSemen, respectively. Morphological discrimination of these two herbal medicines is difficultbecause the seeds of the Brassica species have similar shapes. Since the descriptions of the differentBrassicae Semen in the Korean and Chinese pharmacopoeia can be confused, it is necessary todevelop an accurate method for identification of the different species. Therefore, DNA barcodes ofsix Brassica species, B. juncea, B. napus, B. nigra, B. oleracea, B. rapa, and Sinapis alba, collectedfrom various locations and markets, were analyzed to develop a molecular marker for distinguishingBrassicae Semen and Brassicae Campestris Semen. Nucleotide sequence comparison and phylogeneticanalysis of internal transcribed spacer (ITS) regions based on the amphidiploid types and U'striangle provide useful genetic information for the identification of these two herbal medicines andBrassica species. However, the sequences of the chloroplast maturase K (matK) gene showedspecies-specific insertions and deletions or substitutions only for B. nigra, B. oleracea, and S. albabut not for B. juncea, B. napus, and B. rapa. The use of genome-specific marker nucleotides in ITSregions provide an objective and accurate method for authentication of Brassica species andvaluable information for further molecular marker development. 배추속(Brassica)에 속하는 갓과 유채는 유지 및 사료작물 등 다방면으로 이용되며 그 종자는 개자와 운대자라는 한약재로사용되는 경제적으로 중요한 작물이다. 배추속 식물의 종자는 형태적으로 유사하여 개자와 운대자의 경우 형태적 종 감별에 어려움이 있다. 또한 우리나라 대한약전과 중국약전에서 개자에 대한 규정에 차이가 있어 이로 인하여 개자와 백개자가 혼용될우려가 있기 때문에 정확한 동정방법이 필요한 현실이다. 본 연구는 국내·외 다양한 지역에서 수집되거나 현재 유통되고 있는갓(B. juncea), 유채(B. napus), 흑갓(B. nigra), 양배추(B. oleracea), 배추(B. rapa), 그리고 백겨자(Sinapis alba)를 분석하여개자 및 운대자의 종을 구별할 수 있는 유전자 마커를 개발하기 위해 수행하였다. ‘우장춘의 삼각형’에 따라 복이배체 type을확인할 수 있는 ITS 부위의 염기서열 비교와 계통 분석을 통하여 ITS 부위가 두 약재의 감별 및 배추속의 종 동정에 유용한 유전적 정보를 제공한다는 것을 확인하였다. 하지만 matK 유전자의 경우에는 흑갓, 양배추, 백겨자 3종을 구분할 수 있는 염기치환은 존재하였으나, 갓, 유채, 배추에서는 종 특이적인 염기삽입/결실 및 치환이 나타나지 않았다. 따라서 ITS 부위의 각 genome특이적인 marker nucleotide를 이용하여 개자 및 운대자의 객관적이고 정확한 종 동정이 가능하며, 향후 분자마커 개발에 유용한 정보로 활용할 수 있을 것으로 기대된다.