• Fisheries and Aquatic Sciences
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• 제7권3호
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• pp.130-135
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• 2004

The marine dinoflagellate genus Alexandrium, which produces PSP toxins, has a global distribution. As human-assisted dispersal of the species has been suggested, it is important to develop molecular tools to trace the dispersal pathway. To screen population-specific DNA sequences that differentiate Korean and Japanese A. catenella, we targeted the area downstream of the chloroplast psbA gene using PCR with population-specific DNA primers followed by RFLP (restriction fragment length polymorphism) analysis and sequencing. The RFLP patterns of the PCR products divided Korean and Japanese A. catenella regional isolates into three types: Korean, Japanese, and type CMC3, isolated from Korea. We sequenced the PCR products, but found no similar gene in a homology search. The molecular phylogeny inferred from the sequences separated the Korean and Japanese A. catenella strains, as did the RFLP patterns. However, the Japanese isolates included two slightly different sequences (types J and K), while the Korean sequence was the same as the Japanese K type. In addition, a unique sequence was found in the Korean strains CMC2 and CMC3. Population-specific PCR amplification with Japanese A. catenella type-specific PCR primers designed from the type J sequence yielded PCR products for Japanese strains only, showing that the unknown gene can be used for a population analysis of Korean and Japanese A. catenella.

• 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.

• 한국어병학회지
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• 제19권2호
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• pp.141-153
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• 2006

Genomic DNA samples isolated from two geographical crayfish (Cambaroides similis) populations in the inland of the Korean Peninsula, at Jeonju (Jeonju crayfish; JJC) and Jeongup (Jeongup crayfish; JUe), were PCR-amplified repeatedly. The six arbitrarily selected primers OPC-03, OPC-06, OPC-09, URP-02, URP07 and URP-09 generated the common, specific, and polymorphic fragments. The sizes of DNA fragments also varied widely, from 100 bp - 2,600 bp. Here, 521 fragments were identified in the JJC population, and 354 in the JUC population: 6 primers generated 60 specific fragments (60/521 fragment, 11.5%) in the JJC population, and 90 (90/354 fragments, 25.4%) in the JUC population. These primers produced 42 polymorphic fragments (8.1%) in the DC population, and 18 (5.1%) in the mc population. Especially these results demonstrate that the primers detected numerous specific fragments. Especially, the decamer primer OPC-06 generated inter-population-common DNA fragments, approximately 400 and 800 bp, respectively, in both the JJC and JUC populations. The universal primer URP-02 also generated inter-population-identical DNA fragments, approximately 350 bp and 600 bp, between the two geographical crayfish populations. Based on the average bandsharing values of all samples, the bandsharing value of individuals within the JJC population was much higher than in the JUC population. The bandsharing value between individuals no. 10 and no. 15 was 0.683, which was the highest between the two geographical populations. The dendrogram obtained by the six primers indicates two genetic clusters: cluster I (CRAYFISH 01 - CRAYFISH II), and cluster 2 (CRAYFISH 12 - CRAYFISH 22). The genetic distance between the two geographical populations ranged from 0.053 to 0.605. Ultimately, the longest genetic distance displaying significant molecular differences was found to exist between individuals in the two crayfish populations, between individuals CRAYFISH no. 02 of Jeonju and CRAYFTSH no. 15 of Jeongup (genetic distance = 0.605).

• 한국패류학회지
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• 제24권1호
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• pp.11-24
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• 2008

GDNA was isolated from the jedo venus clam (Protothaca jedoensis, Lischke) from Boryeong (jedo venus clam from Boryeong JVCB) and Wonsan (jedo venus clam from Wonsan; JVCW) located in the West Sea and the East Sea of Korean Peninsula, respectively and we performed clustering analyses, DNA polymorphisms and the populations genetic variations. In the present study, the seven decamer primer generated the one hundred and eleven major/minor specific bands in JVCB population and ninety four-specific bands in JVCW population. Seven primers generated the unique shared bands to each population of one hundred and seventy-six, on average of 25,1, in JVCB population from Boryeong and three hundred thirty, on average of 47,1, in JVCW population from Wonsan, respectively. The dendrogram obtained by the seven oligonucleotides primers, indicates two genetic clusters. Especially, two Protothaca between the individual WONSAN no. 12 and BORYEONG no. 10 showed the longest genetic distance (0.537) in comparison with other individuals used. Accordingly, RAPD analysis showed that the JVCB was a little more genetically diverse than the JVCW population. This result implies the genetic similarity owing to rearing in the same and/or similar circumstances or inbreeding within the JVCW population. So to speak, JVCB population may have high levels of genomic DNA variability owing to the introduction of the wild individuals from the other sites to sampling sites although it may be the geographically diverse distribution of this species. However, it was confirmed that it did not appear like that really in this study. We feel convinced that RAPD analysis discovered a significant genetic distance between two Protothaca population pairs (P<0.001). The existence of population discrimination and genetic diversity between two Protothaca populations was identified by RAPD analysis.

• 한국어류학회지
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• 제18권4호
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• pp.300-310
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• 2006

한국 서해안의 서천 및 고창지역과 남해안의 부산지역으로부터 채취한 전어(Konosirus punctatus) 3개 집단의 개체로부터 genomic DNA를 분리 추출하여 PCR로 반복해서 증폭시켰다. 8개의 decamer와 20-mer를 사용하여 전체적으로 서천의 전어집단에서 713개의 loci, 부산집단에서 791개 및 고창 전어집단으로부터 732개의 100 bp에서 2,800 bp의 크기에 해당되는 total loci를 얻어냈다. 우리는 서천 전어집단에서 독특한 50개의 unique loci, 부산 전어집단으로부터 70개의 unique loci 그리고 고창의 전어집단으로부터 130개의 unique loci를 각각 확인하였고, 또한 3개 전어집단 모두에 대해서 공통적으로 가지고 있는 120개의 shared loci도 확인하였다. 특이한 specific loci를 확인한 결과 서천 전어집단에서는 108개(15.1%), 부산집단에서는 74개(9.4%) 그리고 고창 전어집단에서는 67개(9.2%)를 각각 얻어냈다. 또한 8개의 primer를 통해서 서천 전어집단에서 48개 (6.7%), 부산 전어집단에서는 26개 (3.3%) 그리고 고창 전어집단에서 16개 (2.2%)의 polymorphic loci를 얻어냈다. Similarity matrix를 통해서 볼 때 서천 전어집단에서 0.756에서 0.936까지, 부산집단에서 0.800에서 0.938까지 그리고 고창 전어집단에서 0.731에서 0.959까지의 공유가(bandsharing value)를 확인하였다. 8개의 primer를 이용하여 얻어진 dendrogram을 통해서 볼 때 genetic cluster는 cluster 1 (SEOCHEON 01~SEOCHEON 10), cluster 2 (BUSAN 11~BUSAN 20과 GOCHANG 23~GOCHANG 24) 그리고 cluster 3 (GOCHANG 21, 22, 25, 26, 27, 28, 29 및 30)와 같이 3개의 cluster로 나누어졌다. 위에서와 같이 고창 전어집단의 일부 개체는 부산 전어집단에 속하는 것으로 나타났으며, 따라서 2 전어집단의 일부 개체들은 부분적으로 오고 가는 이주현상을 나타내는 것으로 사려된다. 이러한 결과를 볼 때 RAPD-PCR 분석 방법을 통해서 우리는 지리적으로 떨어져 있는 3개의 전어 집단에 존재하는 유의성이 있는 유전적 거리를 확인할 수 있었다. 여러 가지 decamer와 20-mer를 이용한 RAPD-PCR 분석 방법은 종 및 지리적 집단과 지리적 전어집단에 존재하는 유전적 다양성, 다형성 및 유전적 유사성을 확인하는데 필요로 하는 독특한 specific/polymorphic marker를 확인할 수 있는 이용 가능한 방법이라고 할 수 있다.

• 한국발생생물학회지:발생과생식
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• 제13권2호
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• pp.97-103
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• 2009

Genomic DNA samples isolated from four geographical freshwater crab (Eriocheir sinensis) populations collected in the inland of the Korean Peninsula (Gunsan, Paju, and Nampo) and a Chinese site, were used for PCR amplification. Seven decamer primers generated 19 specific loci (19/243 loci, 7.81%) in the Gunsan population, 32 (32/215 loci, 14.88%) in the Paju population, 19 (19/231 loci, 8.23%) in the Nampo population and 62 (62/340 loci, 18.24%) in a Chinese population. The average 8.9 specific loci exhibited inter-individual-specific characteristics, thus revealing DNA polymorphisms in the Chinese population. The number of unique shared loci to each population and number of shared loci by the four populations were generated by molecular analysis using seven primers in four populations. 35 unique shared loci to each population, with an average of 5.0 per primer, were observed in the Gunsan population, and 50 loci, with an average of 7.1 per primer, were observed in the Chinese population. The hierarchical dendrogram indicates three main branches: cluster 1 (GUNSAN 01$\sim$GUNSAN 05, PAJU 06$\sim$PAJU 10 and NAMPO 11$\sim$NAMPO 15) and cluster 2 (CHINESE 16, 17, 18, 19 and 20). Conclusively individual no. 20 of the PAJU 10 freshwater crab was most distantly related to CHINESE no. 20 (genetic distance = 0.667). Taken together, these results demonstrate the potential of RAPD analysis to identify diagnostic markers for the identification of four freshwater crab populations.

• 한국어류학회지
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• 제17권3호
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• pp.173-186
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• 2005

한국과 대서양산 갈치 (Trichiurus lepturus) 2지리적 집단으로부터 genomic DNA를 분리 추출하였다. 선택된 8개의 RAPD primer를 이용하여 common, polymorphic 그리고 specific fragment를 얻어냈다. 2지역으로부터 primer간 banding patterns 의 복잡성이 두드러지게 나타났다. DNA fragment 의 분자적 크기는 150 bp에서부터 3,000 bp까지 커다란 차이를 나타내었다. 본 연구에서 한국산 갈치 집단에서는 947개의 fragment가 나타났고, 대서양산 갈치 집단에서는 642개의 fragment 가 확인되었다. 또한 한국산 집단에서는 148개의 specific fragment (15.6%) 가 확인되었으며, 대서양산 갈치집단에서는 61개의 specific fragment (9.5%)가 발생되었다. 한국산 갈치집단에서는 638개의 common fragment가 나타났으며, 이는 primer 당 평균적으로 79.8개의 fragment 로 확인되었다. 또한 대서양산 갈치집단에서는 429개의 common fragment 가 확인되었고, 평균해서 primer 당 53.6개의 common fragment 가 나타났다. 한국산 갈치집단과 대서양산 갈치집단의 polymorphic fragment는 각각 76개와 27개로 확인되었다. 모든 갈치시료의 평균적인 bandsharing value를 기초로 해서 한국산 갈치집단의 similarity matrix를 조사해 본 결과 0.784 로부터 0.922까지 나타났고, 대서양산 갈치집단의 값은 0.833로부터 0.990까지 확인되었다. 결과적으로 대서양산 갈치집단내 개체의 bandsharing value 평균값은 한국산 갈치집단의 평균값보다 높게 나타났다. 8개의 primer를 사용하여 얻어진 dendrogram은 cluster 1 (KOREAN 01~KOREAN 11) 및cluster 2 (ATLANTIC 12~ATLANTIC 22)와 같이 2개의 유전적 클러스터로 나뉘어졌다. 한국산 갈치집단내의 10번째 개체(KOREAN no. 10)와 11번째 개체(KOREAN no. 11) 사이가 가장 가까운 유전적 관계(genetic distance = 0.038)를 나타내었다. 궁극적으로 볼 때 한국산 갈치집단의 1번째(KOREAN no. 01)와 대서양산 갈치집단의 16번째(ATLANTIC no. 16) 개체 사이가 가장 먼 유전적 거리(genetic distance = 0.708)를 나타내었다.

• 한국발생생물학회지:발생과생식
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• 제22권2호
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• pp.193-198
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• 2018

The author undertook PCR-founded genetic platform to investigate the hierarchical dendrogram of Euclidean genetic distances of one razor clam population, particularly for Solen corneus, which was further associated with those of the other clam population, by engaging with the precisely designed oligonucleotide primer sets. Seven oligonucleotides primers were used producing a total of 639 counted bands in population A and 595 in population B, respectively, ranging in size of DNA fragments from larger than approximately 50 bp to less than 1,100 bp. Their primers generated 39 specific fragments (6.10%) in population A and 47 (7.90%) in population B, respectively Comparatively, individuals of one razor clam population were fairly related to that of the other clam population, as shown in the hierarchical dendrogram of Euclidean genetic distances. The analysis of genetic variation between razor clam populations could offer important statistics for fisheries and mariculture. Generally the results showed specific and/or conserved genetic loci between razor clam populations. Specific markers established by the author will be valuable for the genetic analysis, species protection and increase of razor clam individuals in coastal region of the Korean Peninsula.

• 한국패류학회지
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• 제29권3호
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• pp.163-169
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• 2013

In the present study, the seven primers BION-33, BION-34, BION-37, BION-41, BION-44, BION-45 and BION-42 generated the total number of loci, average number of loci per lane and specific loci in Hongseong, Yeosu and Goheung population of F. mutica, respectively. 7 primers generated 19 specific loci in the Hongseong population, 29.3 in the Yeosu population and 23.1 in the Goheung population, respectively. Especially, the decamer primer BION-37 generated 7 unique loci to each population, which were identifying each population, approximately 700 bp in Hongseong population. In this study, the dendrogram obtained by the seven primers indicates three genetic clusters: cluster 1 (HONGSEONG 01-HONGSEONG 07), cluster 2 (YEOSU 08-YEOSU 14) and cluster 3 (GOHEUNG 15-GOHEUNG 21). Among the twenty one cockles, the shortest genetic distance that displayed significant molecular differences was between individuals 17 and 19 from the Goheung population (genetic distance = 0.051), while the longest genetic distance among the twenty-one cockle individuals that displayed significant molecular differences was between individuals HONGSEONG no. 03 and YEOSU no. 12 (genetic distance = 0.616). Relatively, individuals of YEOSU population were fairly closely related to that of GOHEUNG population. Ultimately, PCR fragments revealed of in this study may be useful as a DNA marker the three geographic populations to distinguish.

• Animal Systematics, Evolution and Diversity
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• 제38권4호
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• pp.274-278
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• 2022

One marine ciliate, Diophrys quadrinucleata Zhang et al., 2020 was newly recorded from South Korea in this study. We provided morphological diagnosis and images of the Korean D. quadrinucleata population. We determined the small subunit ribosomal DNA (SSU rDNA) and cytochrome oxidase subunit I (CO1) sequence data of D. quadrinucleata, and then the sequences were compared with other Diophrys species. Intra-specific variation between the Korean and type (Chinese) populations was identical in the SSU rDNA, while the inter-specific variations between seven Diophrys species were 0.3-3.8% in the SSU rDNA and 12.6-18.2% in the CO1. In this study, we obtained 18S and CO1 data from species with identified morphology. As the importance of securing 18S and CO1 based on morphology increases in current studies, this study will contribute to ciliate studies.