• ALGAE
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• 제36권1호
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• pp.13-24
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• 2021

The present-day genetic structure of macroalgal species reflects both geographical history and oceanic circulation patterns as well as anthropogenic introduction across native ranges. To precisely understand the genetic diversity and how the factors shape the current population structure of Gloiopeltis furcata sensu lato, we determined the mitochondrial 5' end of cytochrome c oxidase subunit I (COI-5P) sequences for 677 individuals sampled from 67 sites spanning almost the entire distribution range in Korea and Japan. Results from the phylogenetic analysis and haplotype distribution revealed eleven distinct lineages within G. furcata s.l. along the Korea-Japan coastal areas and displayed divergent phylogeographic patterns among lineages. Despite the closely related lineages distributed in same habitats as high rocky intertidal zone, they display different phylogeographic patterns among lineages. The populations from the south of Korea-Japan harbored the highest genetic diversity and unique endemism in comparison with other populations in the distribution range. This could be the evidence of southern refugia for G. furcata s.l. in the Northwest (NW) Pacific and the recent migration from native to introduced region. The reason is that an exceptional distribution pattern was found high genetic diversity in Hakodate of Japan where is the northern location in the NW Pacific. Our results imply the contemporary influence on the distribution due to current circulation pattern and anthropogenic effects. These phylogeographic findings provide the important insight into cryptic species diversity and the detailed distribution pattern of Gloiopeltis in the NW Pacific.

• ALGAE
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• 제37권2호
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• pp.135-147
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• 2022

The red algal genus Chondrus have long been used as raw materials for carrageenan and dietary fiber in health foods. Despite the importance of genetic information in safeguarding natural seaweed resources, knowledge of the population genetics of Chondrus in the northwest Pacific is limited. In this study, genetic diversity and phylogeographic structure of 45 populations (777 specimens) of Chondrus from Korea, China, and Japan were evaluated based on mitochondrial COI-5P gene sequences, and phylogenetic relationships were confirmed based on plastid rbcL gene sequences. Molecular analyses assigned the specimens in this study to three Chondrus species: C. nipponicus, C. ocellatus, and C. giganteus; phenotype-based species classification was impossible owing to their high morphological plasticity. We found moderate intraspecific genetic diversity and a shallow phylogeographic structure in both for C. nipponicus and C. ocellatus, and low intraspecific genetic diversity in C. giganteus. Each of the three species exhibited high-level intraspecific gene flow among regions based on the most common haplotypes (CN1 for C. nipponicus, CO1 for C. ocellatus, and CG1 for C. giganteus). Our comprehensive genetic information provides insights into the phylogeographic patterns and intraspecific diversity of the economically important Chondrus species. It also highlights the need to conserve existing natural Chondrus resources through continuous monitoring of genetic diversity and phylogeographic pattern.

• Parasites, Hosts and Diseases
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• 제60권6호
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• pp.393-400
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• 2022

Human infection with simian malaria Plasmodium knowlesi is a cause for concern in Southeast Asian countries, especially in Malaysia. A previous study on Peninsular Malaysia P. knowlesi rhoptry associated protein-1 (PkRAP1) gene has discovered the existence of dimorphism. In this study, genetic analysis of PkRAP1 in a larger number of P. knowlesi samples from Malaysian Borneo was conducted. The PkRAP1 of these P. knowlesi isolates was PCR-amplified and sequenced. The newly obtained PkRAP1 gene sequences (n=34) were combined with those from the previous study (n=26) and analysed for polymorphism and natural selection. Sequence analysis revealed a higher genetic diversity of PkRAP1 compared to the previous study. Exon II of the gene had higher diversity (π=0.0172) than exon I (π=0.0128). The diversity of the total coding region (π=0.0167) was much higher than those of RAP1 orthologues such as PfRAP-1 (π=0.0041) and PvRAP1 (π=0.00088). Z-test results indicated that the gene was under purifying selection. Phylogenetic tree and haplotype network showed distinct clustering of Peninsular Malaysia and Malaysian Borneo PkRAP1 haplotypes. This geographical-based clustering of PkRAP1 haplotypes provides further evidence of the dimorphism of the gene and possible existence of 2 distinct P. knowlesi lineages in Malaysia.

• Journal of Microbiology
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• 제44권6호
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• pp.591-599
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• 2006

To address the diversity of cyclodextrin-producing P. graminis strains isolated from wheat roots and rhizospheres of maize and sorghum sown in Australia, Brazil, and France, restriction fragment length polymorphism analysis of part of genes encoding RNA polymerase (rpoB-RFLP) and DNA gyrase subunit B (gyrB-RFLP) was used to produce genetic fingerprints. A phylogenetic tree based on rpoB gene sequences was also constructed. The isolates originated from Brazil could be separated from those from Australia and France, when data from the rpoB-based phylogenetic tree or gyrB-RFLP were considered. These analyses also allowed the separation of all P. graminis strains studied here into four clusters; one group formed by the strains GJK201 and $RSA19^T$, second group formed by the strains MC22.02 and MC04.21, third group formed by the strains TOD61, TOD 221, TOD302, and TOD111, and forth group formed by all strains isolated from plants sown in Cerrado soil, Brazil. As this last group was formed by strains isolated from sorghum and maize sown in the same soil (Cerrado) in Brazil, our results suggest that the diversity of these P. graminis strains is more affected by the soil type than the plant from where they have been isolated.

• 생명과학회지
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• 제16권2호
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• pp.253-258
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• 2006

마늘은 전 세계적으로 분포하는 다년생 초본이다. 마늘은 약리적, 경제적으로 중요한 작물이다. 야생종과 재배종의 유전관계를 ISSR 마커로 조사하였다. 또 ISSR 분석으로 이들 종의 유전적 다양도와 집단구조를 실시하였다. 한국의 세 야생 집단은 분리되어 있고 패치 분포를 보이지만 재배종에 비해 높은 유전적 다양성을 유지하고 있었다. ISS5R 마커로 야생종과 재배종의 계통관계는 잘 분리되었다. 비록 한국내 재배종 마늘이 산마늘에서 진화하였 다는 직접적 증거는 없지만 본 연구 결과 그런 가능성은 시사된다. 또한 야생종 산마늘 집단은 생식질 동정과 재배종 마늘의 진화과정에서 유익하게 쓰일 수 있다.

• Asian-Australasian Journal of Animal Sciences
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• 제29권12호
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• pp.1696-1701
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• 2016

Japanese quail is still used as a model for poultry research because of their usefulness as laying, meat, and laboratory animals. Microsatellite markers are the most widely used molecular markers, due to their relative ease of scoring and high levels of polymorphism. The objective of the research was to determine genetic diversity and population genetic structures of selected Japanese quail lines (high body weight 1 [HBW1], HBW2, low body weight [LBW], and layer [L]) throughout 15th generations and an unselected control (C). A total of 69 individuals from five quail lines were genotyped by fifteen microsatellite markers. When analyzed profiles of the markers the observed ($H_o$) and expected ($H_e$) heterozygosity ranged from 0.04 (GUJ0027) to 0.64 (GUJ0087) and 0.21 (GUJ0027) to 0.84 (GUJ0037), respectively. Also, $H_o$ and $H_e$ were separated from 0.30 (L and LBW) to 0.33 (C and HBW2) and from 0.52 (HBW2) to 0.58 (L and LBW), respectively. The mean polymorphic information content (PIC) ranged from 0.46 (HBW2) to 0.52 (L). Approximately half of the markers were informative ($PIC{\geq}0.50$). Genetic distances were calculated from 0.09 (HBW1 and HBW2) to 0.33 (C and L). Phylogenetic dendrogram showed that the quail lines were clearly defined by the microsatellite markers used here. Bayesian model-based clustering supported the results from the phylogenetic tree. These results reflect that the set of studied markers can be used effectively to capture the magnitude of genetic variability in selected Japanese quail lines. Also, to identify markers and alleles which are specific to the divergence lines, further generations of selection are required.

• 한국작물학회지
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• 제66권4호
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• pp.443-451
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• 2021

Finger millet (Eleusine coracana) is widely cultivated in tropical regions worldwide owing to its high nutritional value. Finger millet is more tolerant against biotic and abiotic stresses such as pests, drought, and salt than other millet crops; therefore, it was proposed as a candidate crop to adapt to climate change in Korea. In 2019, we used expressed sequence tag simple sequence repeat (EST-SSR) markers to evaluate the genetic diversity and structure of 102 finger millet accessions from two geographical regions (Africa and South Asia) to identify appropriate accessions and enhance crop diversity in Korea. In total, 40 primers produced 116 alleles, ranging in size from 135 to 457 bp, with a mean polymorphism information content (PIC) of 0.18225. Polymorphism was detected among the 40 primers, and 13 primers were found to have PIC values > 0.3. Principal coordinate and phylogenetic analyses, based on the combined data of both markers, grouped the finger millet accessions according to their respective collection areas.Therefore, the 102 accessions were classified into two groups, one from Asia and the other from Africa. We have conducted an in-depth study on the finger millet landrace pedigree. By sorting out and using the molecular characteristics of each pedigree, it will be useful for the management and accession identification of the plant resource. The novel SSR markers developed in this study will aid in future genetic analyses of E. coracana.

• Fisheries and Aquatic Sciences
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• 제26권9호
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• pp.569-581
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• 2023

The morphology and genetic identification of Rasbora lateristriata and Rasbora argyrotaenia between cultivated and wild populations has never been reported. This study compares morphology and cytochrome c oxidase (COI) genes between farmed and wild stock Rasbora spp. in Java and Sumatra island, Indonesia. We analyzed the truss network measurement (TNM) characters of 80 fish using discriminant function analysis statistical tests. DNA was extracted from muscle tissue of 24 fish specimens, which was then followed by polymerase chain reaction, sequencing, phylogenetic analysis, fixation index analysis, and statistical analysis of haplotype networks. Basic Local Alignment Search Tool analysis validated the following species: R. lateristriata and R. argyrotaenia from farming (Jogjakarta); Rasbora agryotaenia (Purworejo), R. lateristriata (Purworejo and Malang), Rasbora dusonensis (Palembang), and Rasbora einthovenii (Riau) from natural resources. Based on TNM characters, Rasbora spp. were divided into four groups, referring to four distinct characters in the middle of the body. The phylogenetic tree is divided into five clades. The genetic distance between R. argyrotaenia (Jogjakarta) and R. lateristriata (Malang) populations (0.66) was significantly different (p < 0.05). R. lateristriata (Purworejo) has the highest nucleotide diversity (0.43). R. argyrotaenia from Jogjakarta and Purworejo shared the same haplotype. The pattern of gene flow among them results from the two populations' close geographic proximity and environmental effects. R. argyrotaenia had low genetic diversity, therefore, increasing heterozygosity in cultivated populations is necessary to avoid inbreeding. Otherwise, R. lateristriata (Purworejo) had a greater gene variety that could be used to develop breeding. In conclusion, the middle body parts are a distinguishing morphometric character of Rasbora spp., and the COI gene is more heterozygous in the wild population than in farmed fish, therefore, enrichment of genetic variation is required for sustainable Rasbora fish farming.

• Animal Systematics, Evolution and Diversity
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• 제19권2호
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• pp.297-304
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• 2003

Mitochondrial cytochrome b 유전자를 이용하여 한국에서 채집된 5종을 포함한 올빼미과(Strigidae)의 12속 31종의 계통분석을 하였다. Maximum likelihood 분석과, Kimura two-parameter와 p-distance를 이용하여 유전적 근연 관계를 측정하였다. 본 연구에 이용된 959개의 염기서열 가운데, 459개의 서열에서 변이를 확인하였고, 398개의 서열은 계통학적 정보를 가졌다. 올빼미과는 Clade I (Aegolius) , Clade II (Athene, Micrathene, Glaucidium, Surnia), 그리고 Clade III(Bubo, Nyctea, Pulsatrix, Strix, Otus, Ptilopsis, Ninox) 등 세 개의 그룹으로 나뉘어졌다. 또한 Otus속은 지리적으로 다른 두 개의 그룹으로 분리되는 것이 확인되었다.

• Journal of Microbiology
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• 제43권2호
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• pp.144-151
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• 2005

During the past ten years, Archaea have been recognized as a widespread and significant component of marine picoplankton assemblages. More recently, the presence of novel archaeal phylogenetic lineages has been discovered in coastal marine environments, freshwater lakes, polar seas, and deep-sea hydrothermal vents. Therefore, we conducted an investigation into the archaeal community existing in tidal flat sediment collected from Ganghwa Island, Korea. Phylogenetic analysis of archaeal 16S rDNA amplified directly from tidal flat sediment DNA revealed the presence of two major lineages, belonging to the Crenarchaeota ($53.9\%$) and Euryarchaeota ($46.1\%$) phyla. A total of 102 clones were then sequenced and analyzed by comprehensive phylogenetic analysis. The sequences determined in our samples were found to be closely related to the sequences of clones which had been previously obtained from a variety of marine environments. Archaeal clones exhibited higher similarities ($83.25 - 100\%$) to sequences..from other environments in the public database than did those ($75.22 - 98.46\%$) of previously reported bacterial clones obtained from tidal flat sediment. The results of our study suggest that the archaeal community in tidal flat sediment is remarkably diverse.