• Parasites, Hosts and Diseases
• /
• 제55권1호
• /
• pp.47-54
• /
• 2017

The prevalence of cercarial infection in freshwater snails and their evolutionary trends were studied in Nakhon Nayok province, Thailand. A total of 2,869 individual snails were examined for parasitic infections. The results showed that 12 snail species were found to host larval stages of trematodes with an overall prevalence of 4.7%. The infected specimens included 7 types at the cercarial stage; cercariae, megalurous cercariae, echinostome cercariae, furcocercous cercariae, parapleurolophocercous cercariae, virgulate cercariae, and xiphidiocercariae. Regarding molecular identification, ITS2 sequence data of each larval trematode were analyzed, and a dendrogram was constructed using the neighbor-joining method with 10,000 replicates. The dendrogram was separated into 6 clades (order/family), including Echinostomatida/Echinostomatidae, Echinostomatida/Philophthalmidae, Opisthorchiida/Heterophyidae, Plagiorchiida/Prosthogonimidae, Plagiorchiida/Lecithodendriidae, and Strigeatida/Cyathocotylidae. These findings were used to confirm morphological characteristics and evolutionary trends of each type of cercariae discovered in Nakhon Nayok province. Furthermore, this investigation confirmed that the ITS2 data of cercariae could be used to study on phylogenetic relationships or to determine classification of this species at order and/or family level when possible.

• Animal Systematics, Evolution and Diversity
• /
• 제19권2호
• /
• pp.297-304
• /
• 2003

Mitochondrial cytochrome b 유전자를 이용하여 한국에서 채집된 5종을 포함한 올빼미과(Strigidae)의 12속 31종의 계통분석을 하였다. Maximum likelihood 분석과, Kimura two-parameter와 p-distance를 이용하여 유전적 근연 관계를 측정하였다. 본 연구에 이용된 959개의 염기서열 가운데, 459개의 서열에서 변이를 확인하였고, 398개의 서열은 계통학적 정보를 가졌다. 올빼미과는 Clade I (Aegolius) , Clade II (Athene, Micrathene, Glaucidium, Surnia), 그리고 Clade III(Bubo, Nyctea, Pulsatrix, Strix, Otus, Ptilopsis, Ninox) 등 세 개의 그룹으로 나뉘어졌다. 또한 Otus속은 지리적으로 다른 두 개의 그룹으로 분리되는 것이 확인되었다.

• Journal of Microbiology and Biotechnology
• /
• 제15권5호
• /
• pp.1110-1114
• /
• 2005

Six viruses of the genera Carlavirus (Garlic mosaic virus, GarMV, and Garlic latent virus, GarLV), Allexivirus (Garlic virus X, GarV-X, and Garlic mite-borne filamentous virus, GarMbFV) and Potyvirus (Leek yellow stripe virus, LYSV, and Onion yellow dwarf virus, OYDV) from Korean garlic plants with mosaic symptoms were simultaneously detected by multiplex RT-PCR and subsequently sequenced. An immunocapture RT-PCR for the detection of GarLV, LYSV, and OYDV was also performed. The coat protein phylogenetic analysis of the garlic viruses showed that the Korean isolates were most closely related to the isolates from China, Japan, Brazil, and Argentina. This study is the first report for the differentiation of six garlic viruses in Korea by simultaneous detection using multiplex RT-PCR.

• International Journal of Oral Biology
• /
• 제38권1호
• /
• pp.29-36
• /
• 2013

Mitis group streptococci (MGS) were classified based on the nucleotide sequences 16S rRNA gene (16S rDNA) and comprised 13 Streptococcus species. However, 16S rDNA homogeneity among MGS was too high to discriminate between clinical strains at the species level, notably between Streptococcus mitis, Streptococcus oralis, Streptococcus pneumoniae, and Streptococcus pseudopneumoniae. The purpose of this study was to discriminate between 37 strains of MGS isolated from Korean oral cavities using phylogenetic analysis of the DNA-dependant RNA polymerase beta-subunit gene (rpoB). 16S rDNA and rpoB from clinical strains of MGS were sequenced using the dideoxy chain termination method and analyzed using MEGA version 5 software. The resulting phylogenetic data showed that the rpoB sequences could delineate clinical strains of MGS at the species level. Phylogenetic analysis of rpoB is therefore a useful approach for identifying MGS at the species level.

• ALGAE
• /
• 제22권1호
• /
• pp.1-10
• /
• 2007

To gain insights into the phylogenetic relationships of genus Staurastrum and Staurodesmus, we analyzed nuclearencoded small subunit rDNA of 82 strains, and chloroplast atpB gene sequences of 44 strains belonging to three genera (Staurastrum, Staurodesmus, Cosmarium). Excluding the Staurastrum muticum and S. orbiculare, forty five strains of genus Staurastrum formed a well supported clade. It was shown that with no cell wall sculpture and processes, these two species have a strong phylogenetic relationship with genus Staurodesmus. Therefore, it is strongly recommended to transfer Staurastrum without processes and cell wall sculpture into Staurodesmus. S. obsoletus is a taxa that is transferred from Cosmarium. But, from this study, it has shown a phylogenetic relationship with Cosmarium. Therefore, this species is strongly recommended to transfer back to Cosmarium instead of Staurodesmus. As it was studied before, genus Staurastrum has shown monophyletic. Since the genus taurodesmus groups with Cosmarium, they were shown to be polyphyletic.

• Journal of Microbiology
• /
• 제43권2호
• /
• pp.144-151
• /
• 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
• /
• 제28권4호
• /
• pp.341-356
• /
• 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.

• 한국동물위생학회지
• /
• 제38권1호
• /
• pp.51-56
• /
• 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.

• Animal cells and systems
• /
• 제4권1호
• /
• pp.77-85
• /
• 2000

This study has demonstrated the molecular variation of 5S rRNA genes in 15 Allium subgenus Rhizirideum and 1 Allium subg. Allium. For cloning of the 5S rRNA genes, PCR products were obtained from amplification with oligonucleotide primers which were derived from the conserved coding region of 5S rRNA genes. These amplified PCR products were cloned and identified by FISH and sequence analysis. The 5S rRNA loci were primarily located on chromosomes 5 and/or 7 in diploid species and various chromosomes in alloploid species. The size of the coding region of 5S rRNA genes was 120 bp in all the species and the sequences were highly conserved within Allium species. The sizes of nontranscribed spacer (NTS) region were varied from 194 bp (A. dektiude-fustykisum, 2n=16) to 483 bp (A. sativum). Two kinds of NTS regions were observed in A. victorialis var. platyphyllum a diploid, A. wakegi an amphihaploid, A. sacculiferum, A. grayi, A. deltoide-fistulosum and A. wenescens all allotetraploids, while most diploid species showed only one NTS region. The species containing two components of NTS region were grouped with different diploid species in a phylogenetic tree analysis using the sequences of 5S rRNA genes and adjacent non-coding regions.

• Mycobiology
• /
• 제44권4호
• /
• pp.191-201
• /
• 2016

In this study, the phylogeny and morphology of Mycosphaerella nawae (Dothideomycetes, Ascomycota) were examined using Korean and Japanese isolates, to establish the phylogenetic relationship between M. nawae and its allied species. Korean and Japanese isolates of M. nawae were collected from circular leaf spot-diseased leaves and were confirmed based on internal transcribed spacer (ITS) sequence data. Phylogenetic analysis was conducted using multiple genes, including the ITS region, 28S rDNA, ${\beta}-tubulin$, translation elongation $factor-1{\alpha}$, and actin genes. Our results revealed that M. nawae is closely related to members of the genus Phaeophleospora but are distant from the Ramularia spp. In addition, microscopic analysis revealed pseudothecia on the adaxial and abaxial surface of overwintered diseased leaves (ODL) and only on the abaxial surface of diseased leaves. Ascospores are oval to fusiform, one-septate, tapered at both ends, $1.7{\sim}3.1{\times}8.1{\sim}14.1{\mu}m$, and were observed in ODL. Conidia are oval, guttulate, one-septate, $3.5{\sim}4.9{\times}12.8{\sim}19.8{\mu}m$, and barely discernable on 30-day cultures. To our knowledge, this is the first report on the phylogeny of M. nawae, which is closely related to the genus Phaeophleospora, especially P. scytalidii.