• Korean Journal of Plant Taxonomy
• /
• v.37 no.2
• /
• pp.115-129
• /
• 2007

Using internal transcribed spacer (ITS) sequences and inter-simple sequence repeats (ISSRs) data, genetic diversity of a rare species, Hibiscus hamabo Siebold & Zucc. was examined for 3 populations in Jeju Island, Korea. A total of 14 nucleotide (excluding 3 ambiguous nucleotide) site variation in the ITS was observed from 18 individuals (Population 1, Hadori), which differed up to 13 bp in pair-wise comparison. On the contrary, the ITS sequences of all individuals in Populations 2 and 3 were identical. Genetic diversity estimates including Nei's gene diversity (h) generated by ISSR data were substantially high in Population 1 compared to other two populations. Low genetic variation in Populations 1 and 2 is considered due to genetic drift (bottleneck effect) and limited gene flow in these populations. Considering the differences in genetic diversity, protection of the Population 1(Hadori) is very critical for in situ conservation of Hibiscus hamabo in Korea. If ex situ conservation is required, making the full use of Population 1 will be most efficient.

• Korean Journal of Plant Taxonomy
• /
• v.40 no.2
• /
• pp.118-129
• /
• 2010

A taxonomic study of Viola albida complex, containing the representative individuals of three taxa, V. albida var. albida, V. albida var. chaerophylloides, and V. albida var. takahashii, was done based on RAPD data. The amplified loci were 476 in total; obtained with 68 universal primers on seven OTUs. Nei's genetic dissimilarity appeared relatively low within individuals of V. albida var. albida and V. albida var. chaerophylloides (0.118-0.171 and 0.051 respectively), however, it was higher in individuals of V. albida var. takahashii (0.348). On the other hand, there is no specific trend in terms of genetic dissimilartiy among taxa, such as between individuals of V. albida var. albida and V. albida var. takahashii, between those of V. albida var. albida and V. albida var. chaerophylloides, and between those of V. albida var. albida and V. albida var. takahashii. The similarity of OTUs studied is high in clustering analysis, so that this result is compatible with the establishment of this complex. All OTUs are clustered within two groups. The individuals of V. albida var. takahashii, however, are clustered both to the group of V. albida var. albida and to the group of V. albida var. chaerophylloides, meaning that the genetic difference is high which would be commensurate with their morphological variations.

• Asian-Australasian Journal of Animal Sciences
• /
• v.31 no.5
• /
• pp.738-747
• /
• 2018

Objective: In a previous study, analysis of Illumina sequenced metagenomic DNA data of bacteria in Vietnamese goats' rumen showed a high diversity of putative lignocellulolytic genes. In this study, taxonomy speculation of microbial community and lignocellulolytic bacteria population in the rumen was conducted to elucidate a role of bacterial structure for effective degradation of plant materials. Methods: The metagenomic data had been subjected into Basic Local Alignment Search Tool (BLASTX) algorithm and the National Center for Biotechnology Information non-redundant sequence database. Here the BLASTX hits were further processed by the Metagenome Analyzer program to statistically analyze the abundance of taxa. Results: Microbial community in the rumen is defined by dominance of Bacteroidetes compared to Firmicutes. The ratio of Firmicutes versus Bacteroidetes was 0.36:1. An abundance of Synergistetes was uniquely identified in the goat microbiome may be formed by host genotype. With regard to bacterial lignocellulose degraders, the ratio of lignocellulolytic genes affiliated with Firmicutes compared to the genes linked to Bacteroidetes was 0.11:1, in which the genes encoding putative hemicellulases, carbohydrate esterases, polysaccharide lyases originated from Bacteroidetes were 14 to 20 times higher than from Firmicutes. Firmicutes seem to possess more cellulose hydrolysis capacity showing a Firmicutes/Bacteroidetes ratio of 0.35:1. Analysis of lignocellulolytic potential degraders shows that four species belonged to Bacteroidetes phylum, while two species belonged to Firmicutes phylum harbouring at least 12 different catalytic domains for all lignocellulose pretreatment, cellulose, as well as hemicellulose saccharification. Conclusion: Based on these findings, we speculate that increasing the members of Bacteroidetes to keep a low ratio of Firmicutes versus Bacteroidetes in goat rumen has resulted most likely in an increased lignocellulose digestion.

• The Korean Journal of Malacology
• /
• v.32 no.3
• /
• pp.185-188
• /
• 2016

PANM-DB (version 1.0) was constructed as a web-based interface for the analysis and annotation of Next-Generation Sequencing (NGS) data of Mollusca, Arthropoda, and Nematoda. The database collected the sequences of Protostomes (Mollusca, Arthropoda, and Nematoda) from the NCBI Taxonomy Browser, and the same were compiled in a multi-FASTA format and stored using the formatdb program. This improved the processing of the RNA-seq sequences in terms of speed and hit percentage. PANM-DB has been successfully used for the transcriptome annotation of butterfly, land snail, and other commercial mollusca. We have improved the database by updating the same with new sequences and version 2.0 contains a total of 7,571,246 protein sequences (two times more as compared to version 1.0). Furthermore, the updated version contains the Cephalopoda database. The constructed web interface is available that independently analyses following these updates that is an improvement of the mollusks BLAST server. The updated version of PANM-DB will be helpful for the analysis of the NGS based sequencing data of non-model species, especially Mollusca, Arthropoda, Nematoda.

• Korean Journal of Plant Taxonomy
• /
• v.50 no.2
• /
• pp.154-165
• /
• 2020

Coastal regions are experiencing habitat changes due to coastal development and global warming. To estimate the future distribution of coastal plants on the Korean Peninsula due to climate change, the potential distribution of ten species of coastal plants was analyzed using the MaxEnt program. The study covered the eastern, western, and southern coastal areas of the Korean Peninsula. We used the distributional data of coastal plants of the East Asian region and the 19 climate variables of WorldClim 2.0. The future potential distribution was estimated using future climate variables projected from three general circulation models (CCSM4, MIROC-ESM, and MPI-ESM-LR), four representative concentration pathways (2.5, 4.5, 6.0, and 8.5), and two time periods (2050 and 2070). The annual mean temperature influenced the estimation of the potential distribution the most. Under predicted future distribution scenarios, Lathyrus japonicus, Glehnia littoralis, Calystegia soldanella, Vitex rotundifolia, Scutellaria strigillosa, Linaria japonica, and Ixeris repens are expected to show contracted distributions, whereas the distribution of Cnidium japonicum is expected to expand. Two species, Salsola komarovii and Carex kobomugi, are predicted to show similar distributions in the future compared to those in the present. The average potential distribution in the future suggests that the effects of climate change will be greater in the west and the south coastal regions than in the east coastal region. These results will be useful baseline data to establish a conservation strategy for coastal plants.

• Ocean and Polar Research
• /
• v.39 no.1
• /
• pp.13-21
• /
• 2017

Temporal changes in the number of zooplankton species are important information for understanding basic characteristics and species diversity in marine ecosystems. The aim of the present study was to estimate the optimal monitoring frequency (OMF) to guarantee and predict the minimum number of species occurrences for studies concerning marine ecosystems. The OMF is estimated using the temporal number of zooplankton species through bi-weekly monitoring of zooplankton species data according to operational taxonomic units in the Tongyoung coastal sea. The optimal model comprises two terms, a constant (optimal mean) and a cosine function with a one-year period. The confidence interval (CI) range of the model with monitoring frequency was estimated using a bootstrap method. The CI range was used as a reference to estimate the optimal monitoring frequency. In general, the minimum monitoring frequency (numbers per year) directly depends on the target (acceptable) estimation error. When the acceptable error (range of the CI) increases, the monitoring frequency decreases because the large acceptable error signals a rough estimation. If the acceptable error (unit: number value) of the number of the zooplankton species is set to 3, the minimum monitoring frequency (times per year) is 24. The residual distribution of the model followed a normal distribution. This model can be applied for the estimation of the minimal monitoring frequency that satisfies the target error bounds, as this model provides an estimation of the error of the zooplankton species numbers with monitoring frequencies.

• Korean Journal of Plant Taxonomy
• /
• v.42 no.4
• /
• pp.260-266
• /
• 2012

Because the embryological features of Jeffersonia dubia are poorly understood, we conducted the first embryological study comparing it to other related genera of Berberidaceae. Important embryological features of J. dubia are as follows: the anther is tetrasporangiate, anther wall formation confirms basic type, glandular tapetum cells are two nucleate, the epidermis persistent, and the endothecium develops fibrous thickenings, anther dehiscence by two valves, meiosis in a microspore mother cell is accompanied by simultaneous cytokinesis, microspore tetrads are usually tetrahedral, pollen grains two cells at the time of anthesis. The ovule is bitegmic, anatropous and crassinucellate, archesporium single celled, development of the embryo sac Polygonum type, a mature embryo sac is ellipsoidal in shape. Endosperm formation is of Nuclear type and embryogeny Onagrad type. Seeds are arillate and seed coat exotestal type. Embryological comparisons showed that Jeffersonia resemble to Epimedium and Vancouveria rather than Berberis and Mahonia in some features, like as number of tapetal cells, cytokinesis in meiosis, and thickness of exotesta. It also resembles to Gymnospermium in mode of anther wall formation, number of tapetal cells, formation of nucellar cap, and nature of antipodal cells. Nevertheless, Jeffersonia and Gymnospermium differ from several other embryological features and molecular data too. Therefore, embryological evidences support that Jeffersonia is closely related with Epimedium and Vancouveria.

• Korean Journal of Plant Taxonomy
• /
• v.43 no.4
• /
• pp.319-331
• /
• 2013

Records found on labels of specimens deposited at Kyoto University (KYO) and references about three Japanese taxonomists, Koidzumi, Gen'ichi (1883-1953), Ohwi, Jisaburo (1905-1977), Kitamura, Siro (1906-2002) were assembled to produce collector's itineraries from 1930 to 1935 in Korea. The quality of data on labels of the specimens varies, but most are only the collector's name and country of collection, often, the locality data are only textual, and the Chinese and Japanese names, as well as the ethnic dialects common to the region, varies widely. It is estimated that approximately 2,000 specimens collected from Korea by three taxonomists are currently held within the collections of Kyoto University herbarium (KYO). Koidzumi, who was the professor of Kyoto University, traversed different northern parts of the country, such as Island Jeju-do, Mt. Keumkang-san, Hamkyongbuk-do during summer (July to August) in 1932, 1933, and 1935. In 1930 and 1932, Ohwi spend three months in the unexplored mountains in northern parts, such as Hamkyeongnam-do, Hamkyeongbuk-do, and Gangwon-do. On the other hand, for two months in the middle of 1935 visited Jeju-do, Mt. Jirisan and travelled through southern parts. Unlike two previous botanists, major collections in Korea by Kitamura took place twice in one major area in northern part and Jeju-do and Mt. Keumgang-san in 1930, 1932, and 1935.

• Korean Journal of Plant Taxonomy
• /
• v.43 no.2
• /
• pp.128-138
• /
• 2013

The conservation status of an endemic perennial herb, Hanabusaya asiatica (Nakai) Nakai (Campanulaceae) was determined by applying the IUCN risk assessment criteria from our field study and available specimen data. Also, the GIS technology was used to develop a species distribution map to calculate the extent of occurrence (EOO) and area of occupancy (AOO) for the taxon. After two years of continuous field studies, 269 mature individuals were found in four localities in 2011, while 216 mature individuals were confirmed in three localities in 2012. Based on the following data, such as EOO (2,742 $km^2$), AOO (76 $km^2$) and estimated population size of mature individuals, the taxon, which is known as 20 localities in Korean peninsula, is evaluated as the category of Endangered (EN). A major difficulty in application of IUCN criteria to Korean rare plants were the lack of essential biological information and understanding the correct knowledge of the IUCN criteria in previous Korean studies. Sound conclusions regarding the conservation status of individual species require more intensive population studies, observations, and applying IUCN assessment procedures correctly.

• Journal of KIISE:Software and Applications
• /
• v.33 no.9
• /
• pp.787-801
• /
• 2006

Ontology merging describes the process of integrating two ontologies into a new ontology. How this is done best is a subject of ongoing research in the Semantic Web, Data Integration, Knowledge Management System, and other ontology-related application systems. Earlier research on ontology merging, however, has studied for developing effective ontology matching approaches but missed analyzing and solving methods of problems of merging two ontologies given correspondences between them. In this paper, we propose a specific ontology merging process and a generic operator, T-MERGE, for integrating two source ontologies into a new ontology. Also, we define a taxonomy of merging conflicts which is derived from differing representations between input ontologies and a method for detecting and resolving them. Our T-MERGE operator encapsulates the process of detection and resolution of conflicts and merging two entities based on given correspondences between them. We define a data structure, MergeLog, for logging the execution of T-MERGE operator. MergeLog is used to inform detailed results of execution of merging to users or recover errors. For our experiments, we used oriental philosophy ontologies, western philosophy ontologies, Yahoo western philosophy dictionary, and Naver philosophy dictionary as input ontologies. Our experiments show that the automatic merging module compared with manual merging by a expert has advantages in terms of time and effort.