• Genomics & Informatics
• /
• v.10 no.3
• /
• pp.206-211
• /
• 2012

DNA barcoding has been widely used in species identification and biodiversity research. A short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) sequence serves as a DNA bio-barcode. We collected DNA barcodes, based on COI sequences from 156 species (529 sequences) of fish, insects, and shellfish. We present results on phylogenetic relationships to assess biodiversity the in the Korean peninsula. Average GC% contents of the 68 fish species (46.9%), the 59 shellfish species (38.0%), and the 29 insect species (33.2%) are reported. Using the Kimura 2 parameter in all possible pairwise comparisons, the average interspecific distances were compared with the average intraspecific distances in fish (3.22 vs. 0.41), insects (2.06 vs. 0.25), and shellfish (3.58 vs. 0.14). Our results confirm that distance-based DNA barcoding provides sufficient information to identify and delineate fish, insect, and shellfish species by means of all possible pairwise comparisons. These results also confirm that the development of an effective molecular barcode identification system is possible. All DNA barcode sequences collected from our study will be useful for the interpretation of species-level identification and community-level patterns in fish, insects, and shellfish in Korea, although at the species level, the rate of correct identification in a diversified environment might be low.

• Korean Journal of Ecology and Environment
• /
• v.54 no.3
• /
• pp.151-155
• /
• 2021

The application of environmental DNA in the domestic ecosystem is also accelerating, but the processing and analysis of the produced data is limited, and doubts are raised about the reliability of the analyzed and produced biological taxa identification data, and the sample medium (target sample, water, air, sediment, Gastric contents, feces, etc.) and quantification and improvement of analysis methods are also needed. Therefore, in order to secure the reliability and accuracy of biodiversity research using the environmental DNA of the domestic ecosystem, it is a process of actively using the database accumulated through ecological taxonomy and undergoing verification procedures, and experts verifying the resolution of the data increased by gene sequence analysis. This is absolutely necessary. Environmental DNA research cannot be solved only by applying molecular biology technology, and interdisciplinary research cooperation such as ecology-taxa identification-genetics-informatics is important to secure the reliability of the produced data, and researchers dealing with various media can approach it together. It is an area in desperate need of an information sharing platform that can do this, and the speed of development will proceed rapidly, and the accumulated data is expected to grow as big data within a few years.

• Korean Journal of Ecology and Environment
• /
• v.51 no.1
• /
• pp.16-28
• /
• 2018

Although physiological and ecological characteristics of cyanobacteria have been studied extensively for decades, unknown areas still remain greater than the already known. Recently, the development of omics techniques based on molecular biology has made it possible to view the ecosystem from a new and holistic perspective. The molecular mechanism of toxin production is being widely investigated, by comparative genomics and the transcriptomic studies. Biological interaction between bacteria and cyanobacteria is also explored: how their interactions and genetic biodiversity change depending on seasons and environmental factors, and how these interactions finally affect each component of ecosystem. Bioinformatics techniques have combined with ecoinformatics and omics data, enabling us to understand the underlying complex mechanisms of ecosystems. Particularly omics started to provide a whole picture of biological responses, occurring from all layers of hierarchical processes from DNA to metabolites. The expectation is growing further that algal blooms could be controlled more effectively in the near future. And an important insight for the successful bloom control would come from a novel blueprint drawn by omics studies.

• Korean Journal of Plant Taxonomy
• /
• v.37 no.3
• /
• pp.309-321
• /
• 2007

Korea national arboretum has worked with the plant taxonomic society of Korea to make the first fully electronic floristic checklist in Korea. The result is an ever-expanding online plant name index containing scientifically authorative, up-to-date information on the approximately 7,000 taxa including cultivars. With 37 contributing taxonomists, KPNI is the largest collaborative research projects ever assembled in Korea. A comprehensive database model for the taxonomic data from literature and other sources is presented, which was devised for the Korea National Plant Index database project (KPNI). Gwangreung database model is based on an approach using entity-relationsip diagram. It encompasses taxa of all ranks, nothotaxa and hybrid formulae, cultivars, full synonymy, basionyms, Korean name, and other nomenclatural information. Ths paper presents an analysis of KPNI work processes and an overview how we are approaching the construction of Gwangreung databaese model. It can help the system engineers of other biological information systems to develop their database based on the accurate and integrative taxonomic database.

• Genomics & Informatics
• /
• v.20 no.1
• /
• pp.12.1-12.7
• /
• 2022

The two complete mitochondrial genomes (mitogenomes) of Paedocypris progenetica, the smallest fish in the world which belonged to the Cyprinidae family, were sequenced and assembled. The circular DNA molecules of mitogenomes P1-P. progenetica and S3-P. progenetica were 16,827 and 16,616 bp in length, respectively, and encoded 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region. The gene arrangements of P. progenetica were identical to those of other Paedocypris species. BLAST and phylogenetic analyses revealed variations in the mitogenome sequences of two Paedocypris species from Perak and Selangor. The circular DNA molecule of P. progenetica yield a standard vertebrate gene arrangement and an overall nucleotide composition of A 33.0%, T 27.2%, C 23.5%, and G 15.5%. The overall AT content of this species was consistent with that of other species in other genera. The negative GC-skew and positive AT-skew of the control region in P. progenetica indicated rich genetic variability and AT nucleotide bias, respectively. The results of this study provide genomic variation information and enhance the understanding of the mitogenome of P. progenetica. They could later deliver highly valuable new insight into data for phylogenetic analysis and population genetics.

• Journal of Internet Computing and Services
• /
• v.19 no.4
• /
• pp.135-150
• /
• 2018

The biological resources research data around the world are not only very critical themselves but should be shared and utilized. Up to now, the biological resources have been compiled and managed individually depending on the purpose and characteristics of the study without any clear standard. So, in this study, the data reference model would be suggested which is applicable in the phase ranging from the start of the construction of the information system and which can be commonly used. For this purpose, the data model of the related information system would be expanded based on the domestic and foreign standards and data control policy so that the data reference model which can be commonly applicable to individual information system would be developed and its application procedure would be suggested. In addition, for the purpose of proving the excellence of the suggested data reference model, the quality level would be verified by applying the Korgstie's data model evaluation model and its level of data sharing with the domestic and foreign standards would be compared. The test results of this model showed that this model is better than the conventional data model in classifying the data into 4 levels of resources, target, activities and performances and that it has higher quality and sharing level of data in the data reference model which defines the derivation and relation of entity.

• Journal of Environmental Policy
• /
• v.13 no.3
• /
• pp.3-19
• /
• 2014

Large-scale unband development resulted from the rapid economic growth in the Republic of Korea has brought about the habitat destruction for the native animals and plants living in forest and farmland. In order to resolve this problem, it is necessary to consider the natural ecosystem as an organism and to preserve the natural ecosystem by managing ecologically significant habitat consistently. Especially, the local governments should be able to establish regional ecologic networks in consideration of the ecological connectivity and the environmental and ecological excellence, and to reflect them into the local development plans. In regard to this, the methods of the regional ecological network establishment was presented, making use of the results including the national ecological network which assessed the ecological connectivity of the nation and the environmental and ecological assessment results of the Environmental Conservation Value Assessment Map which was designed to analyze and assess the national environmental and ecological values quantitatively. Making use of the case of Gyeongsangnam-do; the results presented that the existing national ecological network in the core region has expanded from $2,986km^2$ to $4,049km^2$ and the existing national ecological network in the buffer region has expanded from $2,940km^2$ to $3,006km^2$. Referring to the regional ecological network in the process of the local development plans could contribute to the increase in biodiversity and the integrated local environmental management including the ecosystem preservation.

• Korean Journal of Ecology and Environment
• /
• v.52 no.3
• /
• pp.210-220
• /
• 2019

Population growth and the increase of energy consumption due to civilization caused global warming. Temperature on the Earth rose about $0.7^{\circ}C$ for the last 100 years, the rate is accelerated since 2000. Temperature is a factor, which determines physiological action, growth and development, survival, etc. of the plant together with light intensity and precipitation. Therefore, it is expected that global warming would affect broadly geographic distribution of the plant as well as structure and function ecosystem. In order to understand the effect of global warming on the ecosystem, a study about the effect of temperature rise on germination and growth in the plant is required necessarily. This study was carried out to investigate the effects of experimental warming on the germination and growth of two oak species(Quercus mongolica and Q. serrata) in temperature gradient chamber(TGC). This study was conducted in control, medium warming treatment($+1.7^{\circ}C$; Tm), and high warming treatment ($+3.2^{\circ}C$; Th) conditions. The final germination percentage, mean germination time and germination rate of two oak species increased by the warming treatment, and the increase in Q. serrata was higher than that in Q. mongolica. Root collar diameter, seedling height, leaf dry weight, stem dry weight, root dry weight, and total biomass were the highest in Tm treatment. Butthey were not significantly different in the Th treatment. In the Th treatment, Q. serrata had significantly higher H/D ratio, S/R ratio, and low root mass ratio (RMR) compared with control plot. Q. mongolica had lower RMR and higher S/R ratio in the Tm and Th treatments compared with control plot. Therefore, growth of Q. mongolica are expected to be more vulnerable to warming than that of Q. serrata. The main findings of this study, species-specific responses to experimental warming, could be applied to predict ecosystem changes from global warming. From the result of this study, we could deduce that temperature rise would increase germination of Q. serrata and Q. mongolica and consequently contribute to increase establishment rate in the early growth stage of the plants. But we have to consider diverse variables to understand properly the effects that global warming influences germination in natural condition. Treatment of global warming in the medium level increased the growth and the biomass of both Q. serrata and Q. mongolica. But the result of treatment in the high level showed different aspects. In particular, Q. mongolica, which grows in cooler zones of higher elevation on mountains or northward in latitude, responded more sensitively. Synthesized the results mentioned above, continuous global warming would function in stable establishment of both plants unfavorably. Compared the responses of both sample plants on temperature rise, Q. serrata increased germination rate more than Q. mongolica and Q. mongolica responded more sensitively than Q. serrata in biomass allocation with the increase of temperature. It was estimated that these results would due to a difference of microclimate originated from the spatial distribution of both plants.

• Genomics & Informatics
• /
• v.21 no.3
• /
• pp.39.1-39.15
• /
• 2023

DNA barcoding without assessing reliability and validity causes taxonomic errors of species identification, which is responsible for disruptions of their conservation and aquaculture industry. Although DNA barcoding facilitates molecular identification and phylogenetic analysis of species, its availability in clariid catfish lineage remains uncertain. In this study, DNA barcoding was developed and validated for clariid catfish. 2,970 barcode sequences from mitochondrial cytochrome c oxidase I (COI) and cytochrome b (Cytb) genes and D-loop sequences were analyzed for 37 clariid catfish species. The highest intraspecific nearest neighbor distances were 85.47%, 98.03%, and 89.10% for COI, Cytb, and D-loop sequences, respectively. This suggests that the Cytb gene is the most appropriate for identifying clariid catfish and can serve as a standard region for DNA barcoding. A positive barcoding gap between interspecific and intraspecific sequence divergence was observed in the Cytb dataset but not in the COI and D-loop datasets. Intraspecific variation was typically less than 4.4%, whereas interspecific variation was generally more than 66.9%. However, a species complex was detected in walking catfish and significant intraspecific sequence divergence was observed in North African catfish. These findings suggest the need to focus on developing a DNA barcoding system for classifying clariid catfish properly and to validate its efficacy for a wider range of clariid catfish. With an enriched database of multiple sequences from a target species and its genus, species identification can be more accurate and biodiversity assessment of the species can be facilitated.