• Journal of Microbiology and Biotechnology
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• 제24권9호
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• pp.1189-1195
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• 2014

A strain-specific identification method is required to secure Chlorella strains with useful genetic traits, such as a fast growth rate or high lipid productivity, for application in biofuels, functional foods, and pharmaceuticals. Microsatellite markers based on simple sequence repeats can be a useful tool for this purpose. Therefore, this study developed five novel microsatellite markers (mChl-001, mChl-002, mChl-005, mChl-011, and mChl-012) using specific loci along the chloroplast genome of Chlorella vulgaris. The microsatellite markers were characterized based on their allelic diversities among nine strains of C. vulgaris with the same 18S rRNA sequence similarity. Each microsatellite marker exhibited 2~5 polymorphic allele types, and their combinations allowed discrimination between seven of the C. vulgaris strains. The two remaining strains were distinguished using one specific interspace region between the mChl-001 and mChl-005 loci, which was composed of about 27 single nucleotide polymorphisms, 13~15 specific sequence sites, and (T)n repeat sites. Thus, the polymorphic combination of the five microsatellite markers and one specific locus facilitated a clear distinction of C. vulgaris at the strain level, suggesting that the proposed microsatellite marker system can be useful for the accurate identification and classification of C. vulgaris.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2018년도 춘계학술발표회
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• pp.38-38
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• 2018

The genus Carduus (Asteraceae), containing ca. 90 species, is mainly distributed in Eurasia and Africa. Carduus species are one of the most hazardous invasive species, which causes serious environmental threats and biodiversity damages in North America. Thus, the member of Carduus are targeted for classical biological control in this region. Here, we provide the complete cp genome of Carduus crispus using next-generation sequencing technology. The size of cp genomes of C. crispus is 152,342 bp. It shows a typical quadripartite structure, consisting of the large single copy (LSC; 83,254 bp), small single copy (SSC; 18,706 bp), separated by a pair of inverted repeats (IRs; 25,191 bp). It contains 115 unique genes of which 21 genes duplicated in the IR regions. The cpSSR regions of Carduus species were searched through the complete chloroplast genome sequence using a tandem repeat search tool in Geneious with the parameters set to ${\geq}7$ mononucleotide repeats, ${\geq}4$ di- and trinucleotide repeats, and ${\geq}3$ tetra-, penta-, and hexanucleotide repeats. A total of 22 repeat motifs were identified, which may be useful for molecular identification of Korean Carduus species (C. cripus), and providing a guideline for its conservation.

• Horticulture, Environment, and Biotechnology : HEB
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• 제59권6호
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• pp.889-897
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• 2018

Currently, there is a lack of genetic markers capable of effectively detecting polymorphisms in Clematis. Therefore, we developed new markers to investigate inter- and intraspecific diversity in Clematis. Based on the complete chloroplast genome of Clematis terniflora, simple sequence repeats were explored and primer pairs were designed for all ten adequate repeat regions (cpSSRs), which were tested in 43 individuals of 11 Clematis species. In addition, the nuclear ITS region was sequenced in 11 Clematis species. Seven cpSSR loci were found to be polymorphic in the genus and serve as markers that can distinguish different species and be used in different genetic analyses, including cultivar identification to assist the breeding of new ornamental cultivars.

• 식물분류학회지
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• 제41권4호
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• pp.299-314
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• 2011

분자 마커의 선택은 집단유전학의 연구방법을 결정하는 중요한 고려사항으로, 현재까지 동식물의 집단유전학 연구에는 알로자임, RAPD, RFLP, AFLP, microsatellite, SNP, ISSR 등이 개발되어 주로 사용되고 있다. 이 중 microsatellite는 핵뿐만 아니라 엽록체, 미토콘드리아와 같은 세포소기관의 게놈상에 매우 풍부하게 존재하며, 핵에서 유래된 microsatellite는 높은 다형성을 보이는 공우성 마커로 집단 구조 및 유전적 다양성 연구에서 최근 선호된다. Microsatellite는 보통 1~6 bp의 짧은 서열이 반복된 것으로 각각의 유전자좌에 특화된 프라이머를 사용하여 증폭한다. Microsatellite는 PCR 반응으로 쉽게 유전자형을 분석할 수 있는 장점이 있으나, 종 특이적으로 개발되고 계통적으로 매우 가까운 근연종에게만 적용될 수 있는 단점이 있다. 따라서, 야생식물의 경우 microsatellite 개발에 필요한 게놈 정보가 부족하고 신규 개발비용이 많이 소요되어 적용이 쉽지 않았으나, 점차 개발비용이 낮아지고 있어, 야생식물을 대상으로 한 microsatellite 연구들이 증가하고 있는 추세이다. 따라서, 본 논문에서는 야생식물의 microsatellite를 이용한 분석 기초를 마련하고자 microsatellite 마커의 다양한 개발 및 분석 방법, 진화 모델 및 적용 분야에 대해 소개하고, 유전자형 결정시 잘못된 결론을 도출할 가능성이 높은 부분에 대한 사항들을 지적하여 야생식물의 microsatellite를 이용한 집단유전학적 분석에 도움을 주고자 하였다.

• Journal of Ecology and Environment
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• 제38권1호
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• pp.47-56
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• 2015

Ailanthus altissima, which is recognized as an invasive tree in the Western world, has been widely observed in Japan. To investigate how A. altissima expanded within-population and to new populations within a region, 446 A. altissima trees were sampled from three separate sites (A, B, and C) including 35 distantly positioned patches, with three chloroplast DNA markers and nine nuclear microsatellite markers. We detected 2, 2, and 3 chloroplast haplotypes in sites A, B, and C, respectively. In addition, 271, 40, and 41 nuclear genotypes were detected in sites A, B, and C, respectively. The clonal richness value was 0.85, 0.78, and 0.53 in sites A, B, and C, respectively. Most trees with the same genotypes were distributed in the same patch, indicating that range expansion by asexual reproduction was limited to a maximum of 45 meters. According to autocorrelation analysis, the extent of nonrandom spatial genetic structure was approximately 0-2 km in sites A and C. KINGROUP analyses showed that 812, 74, and 111 nuclear genotype pairs were detected to have kinship in sites A, B, and C, respectively. Most nuclear genotype pairs were detected within the same patches or sites. These results indicate that the number of A. altissima trees gradually increased from seeds, some of which were produced by trees within sites, meaning that this species could regenerate naturally. This shows the need for the future management of A. altissima as an invasive species in Japan.

• Journal of Plant Biotechnology
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• 제50권
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• pp.207-214
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• 2023

Lindera obtusiloba (Lauraceae) is a dioecious tree that is widely distributed in the low-altitude montane forests of East Asia, including Korea. Despite its various pharmacological properties and ornamental value, the genetic diversity and population structure of this species in Korea have not been explored. In this study, we selected 6 nuclear and 6 chloroplast microsatellite markers with polymorphism or clean cross-amplification and used these markers to perform genetic diversity and population structure analyses of L. obtusiloba samples collected from 20 geographical regions. Using these 12 markers, we identified a total of 44 alleles, ranging from 1 to 8 per locus, and the average observed and expected heterozygosity values were 0.11 and 0.44, respectively. The average polymorphism information content was 0.39. Genetic relationship and population structure analyses revealed that the natural L. obtusiloba population in Korea is composed of 2 clusters, possibly due to two different plastid genotypes. The same clustering patterns have also been observed in Lindera species in mainland China and Japan.

• 한국양식학회:학술대회논문집
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• 한국양식학회 2003년도 추계학술발표대회 논문요약집
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• pp.134-135
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• 2003

The geographic expansion of the toxic dinoflagellates genus Alexandrium has been shown to be world wide ranging. The members of the genus Alexandrium ocnstituted of 20-30 species did not show substantial differences in their morphology, which is mostly referred in the 'tamarensis species complex', except some species. Though rDNA sequences variations are very few and pseudogene types are so diverse that it is difficult to use them as the specific markers. In this study, we outlined Korean and Japanese A, tamarense and A. catenella regional isolates by phylogenetic analysis inferred from no cutting alignments of LSU rDNA D1-D2 and SSU rDNA sequences to group these regional isolates. The results were compared to RFLP patterns of PCR products targeted chloroplast DNA. Lastly screening of highly repeated microsatellite DNA which is frequently used for population analysis in eukaryotes was conducted. A. catenella regional strains identified by the sequencing of rDNA D1-D2 domain were divided into at least 3 groups of type E, CMC and Chinese type, divergence root may not be deep comparing with that of A. tamarense whose pseudogenes are very variable. Results of RFLP pattern and the phylogeny of the unknown gene targeting chloroplast showed that Korean and Japanese A. catenella regional isolates were divided into 3 types: Korean, Japanese and the third CMC types. Population-specific PCR amplification with Japanese A. catenella type-specific PCR primers was useful method for population analysis of A. catenella. Various types of satellite sequences such as 5 nucleotides repeats were obtained from A. tamarense and A. catenella. The 5 nucleotides repeats were primed at the both 3'and 5' ends, and these repeats were prominent as longer repeated motifs. This repeated DNA was intercalated as internal sequences containing various types subrepeats. It is expected that these satellite DNA would be a useful molecular population marker through detail comparison among Alexandrium regional isolates to trace their transferring pathway and to prevent their human-associated their regional extents.

• 한국산림과학회지
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• 제104권4호
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• pp.549-557
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• 2015

본 연구에서는 잣나무 엽록체 DNA의 전체 염기서열을 기반으로 엽록체 SSR(chloroplast simple sequence repeat) 영역을 특이적으로 증폭하는 primer를 개발하고 그 특성을 분석하였다. 잣나무 엽록체 DNA에서 총 30개의 SSR 영역을 탐색하였으며, 이들 영역을 증폭하기 위한 30개의 primer를 제작하였다. 모든 primer가 잣나무를 대상으로 PCR 증폭이 가능하였다. 근연종에 대한 primer의 종간 전환률은 잣나무와 동일한 아속(Subgenus Strobus)에 속하는 눈잣나무(100%)와 섬잣나무(97%)에서 가장 높게 나타났다. 반면 소나무아속(Subgenus Pinus)에 속하는 소나무와 구주소나무에서의 종간 전환률은 73%로 비교적 낮게 나타났다. 점봉산 잣나무 집단을 대상으로 조사한 결과 13개의 유전자좌에서 다형성이 관찰되었으며, 평균 haploid 다양도(H)는 0.512로 계산되었다. 다형적 유전자좌로부터 조합된 haplotype의 수(N)는 25개로 확인되었고, haplotype 다양도($H_e$)는 0.992로 매우 높게 나타났다. 집단내 독특하게 관찰되는 haplotype은 22개(88%)로 전체 28개체 중에서 22개체(79%)를 식별하였다. 본 연구에서 개발한 cpSSR primer는 높은 종간 전환률을 나타냄에 따라 소나무속의 근연종, 특히 잣나무아속 수종에 활용 가능성이 높고, 잣나무 유전변이 분석을 위한 충분한 다형성을 제공하는 유용한 표지자로 판단된다.