• Parasites, Hosts and Diseases
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• v.56 no.4
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• pp.371-374
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• 2018

A 3-month-old female Maltese puppy was hospitalized with persistent diarrhea in a local veterinary clinic. Blood chemistry and hematology profile were analyzed and fecal smear was examined. Diarrheal stools were examined in a diagnostic laboratory, using multiplex real-time polymerase chain reaction (PCR) against 23 diarrheal pathogens. Sequence analysis was performed using nested PCR amplicon of 18S ribosomal RNA. Coccidian oocysts were identified in the fecal smear. Although multiplex real-time PCR was positive for Cyclospora cayetanensis, the final diagnosis was Cystoisospora ohioensis infection, confirmed by phylogenetic analysis of 18S rRNA. To our knowledge, this the first case report of C. ohioensis in Korea, using microscopic examination and phylogenetic analysis.

• ALGAE
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• v.20 no.1
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• pp.1-13
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• 2005

The taxonomic status of three closely related species of the genus Sphacelaria, S. rigidula Kützing, S. fusca (Hudson) C.F Gray and S. didichotoma Saunders was reassessed on the basis of morphological observations from herbarium specimens and phylogenetic analysis of RUBISCO spacer sequences. Sphacelaria rigidula was characterized by having only 2-armed propagules and somewhat slender filaments. Culture experiments revealed that its propagules commonly formed secondary arms, even though they were rarely produced in the field. It is concluded that S. divaricata Montagne characterized by dichotomously branched arms in propagules shoud be synonymized with S. rigidula, based on propagule morphology and measurements. Sphacelaria fusca clearly be separated from S. rigidula by having 2-4 armed propagules. These morphological differences were highly supported by the differences in the RUBISCO spacer sequences. S. didichotoma resembles S. rigidula in having propagules with two dichotomously branched arms. However, it commonly produces the secondary arms in the field. Additionally, this species has shorter primary arms than S. rigidula. Phylogenetic analyses supported the distinction of S. didichotoma from S. rigidula. The northwestern Pacific plants, previously recorded as S. divaricata, were recognized as S. didichotoma.

• ALGAE
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• v.31 no.4
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• pp.303-315
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• 2016

Compsopogon specimens collected in China were examined based on morphology and DNA sequences. Five molecular markers from different genome compartments including rbcL, COI, 18S rDNA, psbA, and UPA were identified and used to construct a phylogenetic relationship. Phylogenetic analyses indicated that two different morphological types from China clustered into an independent clade with Compsopogon specimens when compared to other global samples. The Compsopogon clade exhibited robust support values, revealing the affiliation of the samples to Compsopogon caeruleus. Although the samples were distributed in a close geographical area, unexpected sequence divergences between the Chinese samples implied that they were introduced by different dispersal events and from varied origins. It was speculated that Compsopogon originated in North America, a portion of the Laurentia landmass situated in the Rodinia supercontinent at approximately 573.89-1,701.50 million years ago during the Proterozoic era.Although Compsopogonhad evolved for a rather long time, genetic conservation had limited its variability and rate of evolution, resulting in the current monospecific global distribution. Additional global specimens and sequence information were required to increase our understanding of the evolutionary history of this ancient red algal lineage.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.6
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• pp.776-783
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• 2008

In this study, we investigated the genetic diversity and phylogenetic relationship of six duck populations by employing the genetic polymorphisms of 20 microsatellites. The parameters used in this study included number of alleles, average effective numbers of alleles (E) and average rates of heterozygosity of each population. The results showed that all the microsatellite loci were highly polymorphic except that the locus AJ515896 in Muscovy duck was 0. The average PIC (0.762), average h (0.7843) and average E (5.261) of the six duck populations were all high, indicating that the gene polymorphisms and genetic diversity were high. The test of Hardy-Weinberg equilibrium showed that the six populations in this study were all in Hardy-Weinberg disequilibrium. The F-statistic analysis results showed the range of FST was from 0.0205 (AJ515895) to 0.2558 (AJ515896). The mean FST was 0.0936. Phylogenetic study revealed that Peking duck (Z1 and Z4), Shaoxing duck, Cherry Valley duck and Aobaixing duck were clustered in one group, while the Muscovy duck was clustered in one group alone. The phylogenetic relationships among different populations were in accordance with their breeding history and distribution. Our data suggested that the 20 microsatellite loci were effective markers for analysis of genetic relationships among duck populations.

• Journal of Microbiology
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• v.43 no.2
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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.

• The Plant Pathology Journal
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• v.18 no.3
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• pp.109-114
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• 2002

To evaluate the phylogenetic and taxonomic status of the phytoplasmas associated with water dropwort (Oenanthe javanica DC) disease in Korea and Japan, their 16S rDNA was analyzed. DNAs extracted from water dropworts collected in Korea (Kyongnam province) and Japan (Chiba prefecture) affected by witches' broom and yellows were subjected to PCR using phytoplasma-specific primers, which amplified a 1.4-kbp fragment that included the 16S rDNA. Phytoplasmas were characterized by RFLP analysis using AluI, HaeIII, HhaI, KpnI, MseI, and RsaI restriction enzymes and by sequence analysis of the PCR products. The mater dropwort witches'broom (WDWB) and water dropwort yellows (WDY) 16S rDNA sequences were identical and closely related to onion yellows (OY, 99.9% identity), which belong to the aster yellows (AY) 16S-subgroup. However, the KpnI RFLP analyses clearly distinguished the WDY and WDWB phytoplasmas from the OY phytoplasma. The phylogenetic analysis based on 16S rDNA showed that WDWE and WDY phytoplasmas are members of a relatively homogeneous group that evolved from a common ancestor.

• The Plant Pathology Journal
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• v.28 no.4
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• pp.381-389
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• 2012

Molecular characterization of Cucumber mosaic virus (CMV) was done by using samples from tomato and cucurbitaceous plants collected from different locations in the northwest region of Iran. After screening by enzyme-linked immunosorbent assay, 91 CMV-infected samples were identified. Biological properties of eight representative isolates were compared with each other revealing two distinct phenotypes on squash and tomato plants. Phylogenetic analyses based on nucleotide sequences of the coat protein (CP), movement protein (MP) and 2b of the new isolates, together with that of previously reported isolates, led to the placement of the Iranian isolates in subgroups IA and IB according to CP and MP genes, but in subgroup IA according to the 2b gene. These data suggest that reassortment may have been a major event in the evolution of CMV in Iran, and that the Iranian isolates are derived from a common recent ancestor that had passed through a bottleneck event.

• The Plant Pathology Journal
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• v.28 no.4
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• pp.341-356
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• 2012

Shiitake (Lentinula edodes) is the most economically important cultivated mushroom, but yields are impacted by its competitor, Trichoderma spp. We previously found two unidentified Trichoderma species growing in bedlogs and sawdust shiitake media in Korea. Here, we identify and re-describe those two species based on molecular sequence data, morphology, and culture characteristics. Well-supported clades based on phylogenetic analyses of internal transcribed spacer, translation elongation factor 1-${\alpha}$, and RNA polymerase subunit II sequences grouped one of the unidentified Trichoderma spp. with Hypocrea pseudogelatinosa and the other with Hypocrea pseudostraminea, and their morphologies matched well with the original descriptions of the two Hypocrea species. This study reports the first phylogenetic analyses of H. pseudogelatinosa and Japanese strains of H. pseudostraminea. Based on the phylogenetic results, we redescribed these two species using modern taxonomic concepts in Hypocrea/Trichoderma.

• Korean Journal of Veterinary Service
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• v.38 no.1
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• pp.51-56
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• 2015

Infectious bronchitis virus (IBV) causes an acute and highly contagious viral disease of chicken that is great economic losses to the poultry industry worldwide. Among the IBV structural proteins, the high rate spike glycoprotein S1 gene mutation and antigenic variant strains have been reported in many countries. During the years 2012~2014, 10 IBV strains were isolated from infected chicken farms distributed in provinces of Jeonbuk. Analysis of the S1 gene sequences amplified from 10 isolated strains with QX strains showed nucleotide homologies ranging from 96.5 to 95.4%. Phylogenetic analysis revealed that all strains were clustered into QX-like groups. This study suggests that QX-like IBVs are circulating in commercial chicken farms in Jeonbuk. Therefore, the continuing survellance is significantly important for prevention and control of BIV infection.

• Journal of Microbiology
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• v.41 no.2
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• pp.152-156
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• 2003

Through enrichment on two nutrient agars, 57 Thermus isolates were recovered from 15 hot spring samples taken from the Rehai geothermal area, Tengchong, China. Unique growth characteristics were observed when the strains were transferred from YIM14 medium to Thermus medium. Phylogenetic analysis showed that the 16S rDNA sequences of the isolates and clones from the Rehai geothermal area farmed a monophyletic group on the phylogenetic tree. A secondary structure comparison showed that their 16S rRNAs have unique secondary structure characteristics.