• Molecules and Cells
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• 제27권2호
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• pp.205-209
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• 2009

The loci of the 5S and 45S rRNA genes were localized on chromosomes in five species of Capsicum, namely, annuum, chacoense, frutescens, baccatum, and chinense by FISH. The 5S rDNA was localized to the distal region of one chromosome in all species observed. The number of 45S rDNA loci varied among species; one in annuum, two in chacoense and frutescens, and chinense, and four in baccatum, with the exceptions that 'CM334' of annuum had three loci and 'tabasco' of frutescens gad one locus. 'CM334'-derived BAC clones, 384B09 and 365P05, were screened with 5S rDNA as a probe, and BACs 278M03 and 262A23 were screened with 25S rDNA as a probe. Both ends of these BAC clones were sequenced. FISH with these BAC probes on pachytenes from 'CM334' plant showed one 5S rDNA locus and three 45S rDNA loci, consistent with the patterns on the somatic chromosomes. The 5S rDNA probe was also applied on extended DNA fibers to reveal that its coverage measured as long as 0.439 Mb in the pepper genome. FISH techniques applied on somatic and meiotic chromosomes and fibers have been established for chili to provide valuable information about the copy number variation of 45S rDNA and the actual physical size of the 5S rDNA in chili.

• 한국환경복원기술학회지
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• 제22권6호
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• pp.125-138
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• 2019

This study aims to highlight the possibility in identifying species composition of fish communities using the environmental DNA (eDNA) metabarcoding technique, from both of the technical introduction and the pilot test at urban ecological streams. This new emerging survey technique using eDNA is getting popular in the world as a compensating way for the conventional field survey. However, the application to the domestic cases has yet to be studied. We attempted to use this technique for identifying fish species observed at four survey points in Hwangguji-chon, Suwon City. As a result, the detected number of species by eDNA sampled once in May was significantly matched with the total number of observed species in annual field surveys. Additionally eDNA results indicated the presence possibility of the unobserved species in field last year, even though the validation may be required. This survey technique seems to be more efficient and applicable to diverse situations of the fields and species, thereby needs to be studied further. We discussed the pros and cons of the application and summarized the research directions in future.

• Korean Chemical Engineering Research
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• 제62권3호
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• pp.274-280
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• 2024

기계학습법의 신경망 기술을 이용한 자료분석은 질병 유전자 탐색 및 진단, 신약 개발, 약인성 간 손상 예측 등과 같은 다양한 분야에서 활용되고 있다. 질병 특징 발견을 위한 자료분석은 DNA 정보를 기반으로 이루어질 수 있다. 본 연구에서는 DNA의 분자 정보 중 DNA의 길이와 용액 내 DNA의 길이별 종 개수를 예측하는 신경망을 개발하였다. 겔 전기영동을 통한 기존 방법론의 시간 소요 한계점을 해결하고자, 미세유체역학적 농축 장치의 동역학 자료를 분석 대상으로 하여 실험 분석 과정 중의 시간 소요 문제점을 해결하였다. 동역학 자료를 공간시간 지도로 재구성하여 학습 및 예측에 필요한 계산용량을 낮추었으며, 공간시간 지도에 대한 분석 정확도를 높이기 위해 합성곱 신경망을 활용하였다. 그 결과, 단일 변수 회귀로써의 단일 DNA 길이 예측과 복합 변수 회귀로써의 다종 DNA 길이의 동시 예측 및 이진 분류로써의 DNA 혼합 종 개수 예측을 성공적으로 수행하였다. 추가적으로, 예측 과정 중 발생할 수 있는 예측 편향을 학습 자료 구성 방식을 통한 해결책을 제시하였다. 본 연구를 활용한다면, 광학 측정 자료를 이용하는 액체생검 기반의 세포유리 DNA 분석 및 암 진단 등의 의학 자료 분석을 효과적으로 수행할 수 있을 것이다.

• 생태와환경
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• 제53권1호
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• pp.63-72
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• 2020

본 연구에서는 멸종위기종이 서식하는 4개 하천(금강, 지천, 황지천, 섬진강)에서 환경유전자(environmental DNA, eDNA)와 보편적 어구를 이용한 조사 방법을 적용하여 지점별 종 다양성을 확인하고, 이를 통해 eDNA의 활용을 고찰하였다. eDNA 조사를 통해서 확인된 종 수는 지점 평균(±표준편차) 19종(±4.4)이며, 이는 어구를 이용한 정량 조사의 10종(±4.8)과 비교하여 높게 나타났다. 대부분의 지점에서 eDNA 조사가 어구를 이용한 조사보다 효율이 높게 나타났다. 반면 eDNA 조사 결과 고유종 및 근연종에 대해서 동정의 오류가 확인되어, universal primer (MiFish primer set)에 대한 국내 적용의 한계를 확인하였다. 또한 멸종위기종의 서식 여부도 일부 종에 대해서 eDNA 조사 결과가 현장 조사 및 문헌과의 차이를 보였다. 현재 개발된 universal primer는 국내에서 서식하는 모든 담수종의 서식을 확인하는 데 있어서 결과의 신뢰성을 담보할 수 없기 때문에 universal primer의 보완 및 개발이 필요하며, 멸종위기종과 같은 특정종의 서식 확인을 위해서는 종특이적 마커 개발을 통한 적용이 고려되어야 한다. 마지막으로 eDNA의 현장 조사 방법에 대한 매뉴얼이 개발될 경우, 수생태계 조사에 대한 활용성이 증대될 수 있을 것이다.

• ALGAE
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• 제37권4호
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• pp.281-291
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• 2022

Quantifying the abundance of Chattonella species is necessary to effectively manage the threats from ichthyotoxic raphidophytes, which can cause large-scale mortality of aquacultured fish in temperate waters. The identification and cell counting of Chattonella species have been conducted primarily on living cells without fixation by light microscopy because routine fixatives do not retain their morphological features. Species belonging to the Chattonella marina complex, including C. marina and C. marina var. ovata, had high genetic similarities and the lack of clear morphological delimitations between the species. To estimate the abundance of C. marina complex in marine plankton samples, we developed a protocol based on the droplet digital polymerase chain reaction (ddPCR) assay, with C. marina complex-specific primers targeting the internal transcribed spacer (ITS) region of the rDNA. Cell abundance of the C. marina complex can be determined using the ITS copy number per cell, ranging from 25 ± 1 for C. marina to 112 ± 7 for C. marina var. ovata. There were no significant differences in ITS copies estimated by the ddPCR assay between environmental DNA samples from various localities spiked with the same number of cells of culture strains. This approach can be employed to improve the monitoring efficiency of various marine protists and to support the implementation of management for harmful algal blooms, which are difficult to analyze using microscopy alone.

• Journal of Ecology and Environment
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• 제48권1호
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• pp.32-48
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• 2024

Background: Longitudinal connectivity in river systems strongly affects biological components related to ecosystem functioning, thereby playing an important role in shaping local biodiversity and ecosystem health. Environmental DNA (eDNA)-based metabarcoding has an advantage of enabling to sensitively diagnose the presence/absence of species, becoming an efficient/effective approach for studying the community structure of ecosystems. However, little attention has been paid to eDNA-based biomonitoring for river systems, particularly for assessing the river longitudinal connectivity. In this study, by using eDNA we analyzed and compared species diversity and composition among artificial barriers to assess the longitudinal connectivity of the fish community along down-, mid- and upstream in the Hotancheon from the Geum River basin. Moreover, we investigated temporal variation in eDNA fish community structure and species diversity according to season. Results: The results of species detected between eDNA and conventional surveys revealed higher sensitivity for eDNA and 61% of species (23/38) detected in both methods. The results showed that eDNA-based fish community structure differs from down-, mid- and upstream, and species diversity decreased from down to upstream regardless of season. We found that there was generally higher species diversity at the study sites in spring (a total number of species across the sites [n] = 29) than in autumn (n = 27). Nonmetric multidimensional scaling and heatmap analyses further suggest that there was a tendency for community clusters to form in the down-, mid- and upstream, and seasonal variation in the community structure also existed for the sites. Dominant species in the Hotancheon was Rhynchocypris oxycephalus (26.07%) regardless of season, and subdominant species was Nipponocypris koreanus (16.50%) in spring and Odontobutis platycephala (15.73%) in autumn. Artificial barriers appeared to negatively affect the connectivity of some fish species of high mobility. Conclusions: This study attempts to establish a biological monitoring system by highlighting the versatility and power of eDNA metabarcoding in monitoring native fish community and further evaluating the longitudinal connectivity of river ecosystems. The results of this study suggest that eDNA can be applied to identify fish community structure and species diversity in river systems, although some shortcomings remain still need to be resolved.

• 한국수산과학회지
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• 제28권5호
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• pp.649-658
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• 1995

붕넙치과 어류의 종간에 있어서의 유전적 분화정도를 DNA level에서 관찰하기 위하여 참가자미, 문치가자미, 돌가자미, 강가자미의 미토콘드리아 DNA를 분리하고, 6염기인식의 14제한효소로써 절단한 절단단편의 염기치환수를 계산하였다. 1) mtDNA 총염기대수는 4종 모두 17.6kbp 부근으로 나타나 동일한 염기대수를 가지는 것으로 추정되었다. 2) 14종류의 제한효소로써 절단한 절단단편의 pattern으로 4종의 종내 및 종간의 haplotype수를 조사한 결과, 참가자미에서는 10개, 문치가자미에서는 4개, 강가자미에서는 2개, 돌가자미에서는 1개의 haplotype이 관찰되었으며, 종간에 있어서는 공통적인 haplotype가 전혀 관찰되지 않았다. 3) mtDNA의 유전적 변이성을 나타내는 haplotype 다양도 (h)는 참가자미에서 0.588, 문치가자미에서 0.371로 나타나 참가자미에서 높은 변이성을 나타내었다. 4) 4종의 유전적 분화의 정도를 mtDNA haplotype간의 제한 부위당 염기치환수 (d)로써 살펴 본 결과, 종내의 평균은 0.0045, 종간의 평균은 0.0344, 속간의 평균은 0.0457로 되어 종간, 속간의 값이 종내에 비해 현저하게 높은 수치를 나타내었다. 5) 4종간의 mtDNA haplotype는 1개 또는 2개의 염기치환에 의한 차이가 아니고 유전적 불연속을 나타내었다.

• Proceedings of the National Institute of Ecology of the Republic of Korea
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• 제3권1호
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• pp.54-65
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• 2022

Species distribution models are a useful tool for predicting future distribution and establishing a preemptive response of invasive species. However, few studies considered the possibility of habitat for the aquatic organism and the number of target sites was relatively small compared to the area. Environmental DNA (eDNA) is the emerging tool as the methodology obtaining the bulk of species presence data with high detectability. Thus, this study applied eDNA survey results of Micropterus salmoides and Lepomis macrochirus to species distribution modeling by seasons in the Anyang stream network. Maximum Entropy (MaxEnt) model evaluated that both species extended potential distribution area in October compared to July from 89.1% (12,110,675 m²) to 99.3% (13,625,525 m²) for M. salmoides and 76.6% (10,407,350 m²) to 100% (13,724,225 m²) for L. macrochirus. The prediction value by streams was varied according to species and seasons. Also, models elucidate the significant environmental variables which affect the distribution by seasons and species. Our results identified the potential of eDNA methodology as a way to retrieve species data effectively and use data for building a model.

• 한국환경복원기술학회지
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• 제25권5호
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• pp.77-88
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• 2022

This study aims to understand the relationship between the distribution of fish species in the two water ecosystems and the habitat factors according to the survey period targeting Gwanggyo Lake Park in the city. There are studies on the appearance and distribution of species by applying eDNA to freshwater ecosystems. However, in the domestic, streams are the target, and studies on the relationship between species distribution and habitat environment in two water environments are lacking. We conducted to analyze the species list and relationship with habitat factors using eDNA research in May and October at 21 points in Gwanggyo Lake Park, Suwon City, which were connected to lakes and streams. As a result, there was no species difference in the water environment according to the survey period. However, the total number of reads during the spawning season(May) was 3,126,482, which was more than double that after the spawning season(October). Tolerant species appeared in Woncheon Lake with a slow or stagnant flow, but there was no significant correlation between species and habitat factors depending on the survey period. On the other hand, intermediate and sensitive species appeared in the Woncheon stream with high flow. There was a significant correlation between the low temperature during the spawning season and the high dissolved oxygen content after the spawning season(P<0.001, Tem.: 20.7±2.6℃, DO: 8.6±1.7). It is expected that environmental DNA will be used to survey species and suggest monitoring methods according to the survey period.

• The Plant Pathology Journal
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• 제32권6호
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• pp.500-507
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• 2016

Single-molecule real-time (SMRT) sequencing allows identification of methylated DNA bases and methylation patterns/motifs at the genome level. Using SMRT sequencing, diverse bacterial methylomes including those of Helicobacter pylori, Lactobacillus spp., and Escherichia coli have been determined, and previously unreported DNA methylation motifs have been identified. However, the methylomes of Xanthomonas species, which belong to the most important plant pathogenic bacterial genus, have not been documented. Here, we report the methylomes of Xanthomonas axonopodis pv. glycines (Xag) strain 8ra and X. campestris pv. vesicatoria (Xcv) strain 85-10. We identified $N^6$-methyladenine (6mA) and $N^4$-methylcytosine (4mC) modification in both genomes. In addition, we assigned putative DNA methylation motifs including previously unreported methylation motifs via REBASE and MotifMaker, and compared methylation patterns in both species. Although Xag and Xcv belong to the same genus, their methylation patterns were dramatically different. The number of 4mC DNA bases in Xag (66,682) was significantly higher (29 fold) than in Xcv (2,321). In contrast, the number of 6mA DNA bases (4,147) in Xag was comparable to the number in Xcv (5,491). Strikingly, there were no common or shared motifs in the 10 most frequently methylated motifs of both strains, indicating they possess unique species- or strain-specific methylation motifs. Among the 20 most frequent motifs from both strains, for 9 motifs at least 1% of the methylated bases were located in putative promoter regions. Methylome analysis by SMRT sequencing technology is the first step toward understanding the biology and functions of DNA methylation in this genus.