• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.12 no.3
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• pp.225-233
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• 2007

To verify which loop regions of 18S rRNA gene are suitable as species-specific genetic markers in ciliates, we analyzed the genetic variation of 18S rRNA gene among 9 Euplotes species (Hypotrichia : Ciliophora). In our result, no inter-specific variation was detected from V1, V3 and V5 regions, and the length of V7 and V8 are 44 bp and 79 bp, respectively, which are too short to make genetic marker. In contrast, V2 and V4 may be good candidate segments of species-specific diagnostic molecular markers because these two regions are most variable ($1.75{\sim}20.61%$) and showed good inter-specific phylogeny. Furthermore, the sequences of V2 and V4 are 123 bp and 306 bp, respectively in length which are enough to make species-specific marker.

• Parasites, Hosts and Diseases
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• v.51 no.4
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• pp.401-412
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• 2013

Because of an increased number of Acanthamoeba keratitis (AK) along with associated disease burdens, medical professionals have become more aware of this pathogen in recent years. In this study, by analyzing both the nuclear 18S small subunit ribosomal RNA (18S rRNA) and mitochondrial 16S rRNA gene loci, 27 clinical Acanthamoeba strains that caused AK in Japan were classified into 3 genotypes, T3 (3 strains), T4 (23 strains), and T5 (one strain). Most haplotypes were identical to the reference haplotypes reported from all over the world, and thus no specificity of the haplotype distribution in Japan was found. The T4 sub-genotype analysis using the 16S rRNA gene locus also revealed a clear subconformation within the T4 cluster, and lead to the recognition of a new sub-genotype T4i, in addition to the previously reported sub-genotypes T4a-T4h. Furthermore, 9 out of 23 strains in the T4 genotype were identified to a specific haplotype (AF479533), which seems to be a causal haplotype of AK. While heterozygous nuclear haplotypes were observed from 2 strains, the mitochondrial haplotypes were homozygous as T4 genotype in the both strains, and suggested a possibility of nuclear hybridization (mating reproduction) between different strains in Acanthamoeba. The nuclear 18S rRNA gene and mitochondrial 16S rRNA gene loci of Acanthamoeba spp. possess different unique characteristics usable for the genotyping analyses, and those specific features could contribute to the establishment of molecular taxonomy for the species complex of Acanthamoeba.

• Journal of Species Research
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• v.10 no.1
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• pp.63-71
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• 2021

Anteholosticha bergeri and Bakuella granulifera were isolated from soil samples collected from Muuidong and Songdo-dong, Incheon and confirmed new to South Korea. Including these two newly recorded species, 11 species of Anteholosticha and four species of Bakuella have been recorded in South Korea to date. Anteholosticha bergeri was discriminated from congeners by following characters: cortical granules, 12-16 macronuclei, 5-8 midventral pairs, 2-3 pretransverse cirri, 4-6 transverse cirri, and three dorsal kineties. Bakuella granulifera was identified by cortical granules, 5-11 buccal cirri, 2-5 frontoterminal cirri, 2-5 midventral cirri rows, and 8-12 transverse cirri. The Korean A. bergeri population corresponds to the Austrian population, except for the number of marginal and transverse cirri, and the Korean B. granulifera population corresponds to the Namibian population, except for body size. In addition, small subunit ribosomal RNA(18S rRNA) gene sequences from both species were determined.

• Animal Systematics, Evolution and Diversity
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• v.38 no.4
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• pp.226-237
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• 2022

Arcuospathidium is a haptorian ciliate genus composed of 18 species, and only one species has been reported in Korea. Here, we identify two unrecorded Arcuospathidium subspecies by morphological observation of both living and protargol-impregnated specimens with the small subunit ribosomal RNA (18S rRNA) gene sequence. These subspecies, Arcuospathidium cultriforme cultriforme (Penard, 1922) Foissner, 1984 and A. cultriforme scalpriforme (Kahl, 1930) Foissner, 2003, were isolated from various terrestrial habitats in July and August 2013, respectivley. Arcuospathidium cultriforme cultriforme is similar to A. cultriforme scalpriforme by a knife-shaped body, a twisted-shaped macronucleus, number of dorsal brushes, position of dorsal brushes, and shape of macronucleus but former mainly differs from the body length to oral bulge length ratio (27-38% vs. 41-53%), extrusome (one types vs. three types), cyst shape (roughly faceted wall vs. smooth surface and thin wall) and number of somatic kinety rows(18-30 vs. 30-44). Additionally, we analyzed the 18S rRNA gene sequences of two A. cultriforme subspecies and compared them with the sequences from GenBank to confirm their identification at the molecular level. As the results of genetic analysis, the 18S rRNA gene sequence of the Korean A. cultriforme cultriforme population is most similar to that of Austrian population. Also, the sequence of the Korean A. cultriforme scalpriforme population is most similar to that of another population with some nucleotide differences.

• Parasites, Hosts and Diseases
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• v.53 no.2
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• pp.237-242
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• 2015

Analysis of ancient DNA (aDNA) extracted from Ascaris is very important for understanding the phylogenetic lineage of the parasite species. When aDNAs obtained from a Joseon tomb (SN2-19-1) coprolite in which Ascaris eggs were identified were amplified with primers for cytochrome b (cyt b) and 18S small subunit ribosomal RNA (18S rRNA) gene, the outcome exhibited Ascaris specific amplicon bands. By cloning, sequencing, and analysis of the amplified DNA, we obtained information valuable for comprehending genetic lineage of Ascaris prevalent among pre-modern Joseon peoples.

• Fisheries and Aquatic Sciences
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• v.21 no.3
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• pp.8.1-8.6
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• 2018

Desmarestia japonica (Phaeophyceae, Desmarestiales) was recently established from the Japanese ligulate Desmarestia and is morphologically similar to D. ligulata. This species has been reported only from Japan. However, the taxonomic reports based on additional regional distributions are needed to clarify this taxonomic entity and its species boundaries. Because Desmarestia species have restricted distributions in Korea, we reexamined herbarium specimens of D. ligulata deposited at the National Institute of Biological Resources (South Korea). To improve the amplification efficiency of the polymerase chain reaction and avoid contamination by the DNA of other organisms, we developed taxon-specific molecular markers suitable for DNA barcoding of Desmarestia species. Nuclear ribosomal small subunit RNA (18S rDNA) and mitochondrial cytochrome c oxidase 1 (cox1) regions were selected as target DNA. As a result, both were successfully isolated from herbarium specimens of D. japonica acquired over 10 years. These molecular markers provide useful genetic information for herbarium specimens for which conventional molecular analysis is challenging.

• Animal Systematics, Evolution and Diversity
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• v.36 no.2
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• pp.113-122
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• 2020

From a moss sample, we isolated and identified Notohymena gangwonensis Kim et al., 2019 based on morphological and molecular data. The moss and type population has completely identical 18S rRNA (nuclear small subunit ribosomal RNA) gene sequences and both are highly similar in morphological and morphometric attributes, except for the diameter and arrangement of the cortical granules. Thus, we reexamined the type materials(i.e., micrographs and gDNA) and resulted in finding mistakes made by the authors of the species. Based on these data and supporting materials newly obtained (i.e., internal transcribed spacer [ITS] 1, ITS2, 5.8S, and partial 28S rDNA sequences, and scanning electron micrographs), we provide improved diagnosis of the species to clarify its identity. In addition, a key for Notohymena species is provided.

• Journal of Life Science
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• v.16 no.1
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• pp.71-75
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• 2006

We analyzed the phylogenic relationships of 23 partial 18S rDNA sequences of 22 species (1 species has 2 strains) belonging to Sarcorptiforms include 4 new sequences, using several tools. Although geographic distributions are quite far from, sequence similarity of two strains of Dermatophygoides pteronyssinus isolated from Japan and New Zealand were very high. This result suggests that mite migration by animals including human occurred in the two continents. We investigated the Endeostigmata taxonomic relationship between the Prostigmata and Oribatida subgroups using small fragments (340-400 bp) of their 185 rDNA sequences. But Endeostigmata was not grouped with Oribatida or Prostigmata. In conclusion, it is first reported phylogenic relationship for classified mites included in Sarcoptiformes using 185 rDNA sequence analysis and its system is a very powerful tool for classification of mites.

• Parasites, Hosts and Diseases
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• v.40 no.1
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• pp.25-31
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• 2002

We describe a riboprinting scheme for identification of unknown Acanthamoeba isolates at the species level. It involved the use of PCR-RFLP of small subunit ribosomal RNA gene (riboprint) of 24 reference strains by 4 kinds of restriction enzymes. Seven strains in morphological group I and III were identified at species level with their unique sizes of PCR product and riboprint type by Rsa 1. Unique RFCP of 17 strains in group II by Dde I. Taq I and Hae III were classified into: (1) four taxa that were identifiable at the species level. (2) a subgroup of 4 taxa and a pair of 2 taxi that were identical with each other. and (3) a species complex of 7 taxa assigned to A. castellanii complex that were closely related. These results were consistent with those obtained by 18s rDNA sequence analysis. This approach provides an alternative to the rDNA sequencing for rapid identification of a new clinical isolate or a large number of environmental isolates of Acanthamoeba.

• Journal of Environmental Health Sciences
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• v.35 no.3
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• pp.187-190
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• 2009

Cryptosporidium spp. were detected in 17 of 135 swine lagoon samples from five farms by 18S ribosomal DNA locus and PCR. Seventeen positive samples identified were included two distinctive genotypes C. suis and Cryptosporidium sp. based on a small-subunit rRNA gene-based PCR-restriction fragment length polymorphism analysis. Cryptosporidium spp. were detected out of farrowing, farrowing and nursery (mix), and finishing. Prevalence rate was 12.6% with infection rates between 3.7 and 18.5%. We concluded that Cryptosporidium oocysts can persist in treated lagoon and potentially contaminate surface water through improper discharge. This study was undertaken for the evaluation of the infection status of the genotypes of Cryptosporidium spp. in swine lagoon.