• Molecules and Cells
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• v.27 no.5
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• pp.515-523
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• 2009

To infer the monophyletic origin and phylogenetic relationships of the order Desmoscolecida, a unique and puzzling group of mainly free-living marine nematodes, we newly determined nearly complete 18S rDNA sequences for six marine desmoscolecid nematodes belonging to four genera (Desmoscolex, Greeffiella, Tricoma and Paratricoma). Based on the present data and those of 72 nematode species previously reported, the first molecular phylogenetic analysis focusing on Desmoscolecida was done by using neighbor joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) methods. All four resultant trees consistently and strongly supported that the family Desmoscolecidae forms a monophyletic group with very high node confidence values. The monophyletic clade of desmocolecid nematodes was placed as a sister group of the clade including some members of Monhysterida and Araeolaimida, Cyartonema elegans (Cyartonematidae) and Terschellingia Iongicaudata (Linhomoeidae) in all the analyses. However, the present phylogenetic trees do not show any direct attraction between the families Desmoscolecidae and Cyartonematidae. Within the monophyletic clade of the family Desmoscolecidae in all of the present phylogenetic trees, there were consistently observed two distinct subgroups which correspond to the subfamilies Desmoscolecinae [Greeffiella sp. + Desmoscolex sp.] and Tricominae [Paratricoma sp. + Tricoma sp].

• International Journal of Industrial Entomology and Biomaterials
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• v.6 no.1
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• pp.87-92
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• 2003

We describe here the cloning, expression and characterization of a cDNA encoding a putative chemosensory protein (CSP) from the mole cricket, Gryllotalpa orientalis. The G. orientalis chemosensory protein cDNA sequences comprised of 384 bp with 128 amino acid residues. The G. orientalis chemosensory protein showed 75.4% protein sequence identity to the Locusta migratoria CSP, Northern blot analysis revealed that signal was stronger in head than leg and cuticle, indicating that the head part containing antennae is a main site for G. orientalis chemosensory protein synthesis. The cDNA encoding G. orientalis chemosensory protein was expressed as approximately 12 kDa polypeptide in baculovirus-infected insect cells.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.221-228
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• 2003

This paper presents a novel method that can identify the individual's haplotype from the given genotypes. Because of the limitation of the conventional single-locus analysis, haplotypes have gained increasing attention in the mapping of complex-disease genes. Conventionally there are two approaches which resolve the individual's haplotypes. One is the molecular haplotypings which have many potential limitations in cost and convenience. The other is the in-silico haplotypings which phase the haplotypes from the diploid genotyped populations, and are cost effective and high-throughput method. In-silico haplotyping is divided into two sub-categories - statistical and computational method. The former computes the frequencies of the common haplotypes, and then resolves the individual's haplotypes. The latter directly resolves the individual's haplotypes using the perfect phylogeny model first proposed by Dan Gusfield [7]. Our method combines two approaches in order to increase the accuracy and the running time. The individuals' haplotypes are resolved by considering the MLE (Maximum Likelihood Estimation) in the process of computing the frequencies of the common haplotypes.

• Animal Systematics, Evolution and Diversity
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• v.28 no.1
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• pp.36-41
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• 2012

The larvae of Chaoborus are widely distributed in lakes, ponds, and reservoirs. These omnivorous Chaoborus larvae are crucial predators and play a role in structuring zooplankton communities, especially for small-sized prey. Larvae of Chaoborus are commonly known to produce predator-induced polyphenism in Daphnia sp. Nevertheless, their taxonomy and molecular phylogeny are very poorly understood. As a fundamental study for understanding the role of Chaoborus in predator-prey interactions in a freshwater ecosystem, the molecular identification and phylogenetic relationship of Chaoborus were analyzed in this study. A molecular comparison based on partial mitochondrial cytochrome oxidase I (COI) between species in Chaoborus was carried out for the identification of Chaoborus larvae collected from 2 localities in Korea. According to the results, the Chaoborus species examined here was identified as C. flavicans, which is a lake-dwelling species. Furthermore, partial mitochondrial genome including COI, COII, ATP6, ATP8, COIII, and ND3 were also newly sequenced from the species and concatenated 5 gene sequences excluding ATP8 with another 9 dipteran species were compared to examine phylogenetic relationships of C. flavicans. The results suggested that Chaoborus was more related to the Ceratopogonidae than to the Culicidae. Further analysis based on complete mitochondrial DNA sequences and nuclear gene sequences will provide a more robust validation of the phylogenetic relationships of Chaoborus within dipteran lineages.

• ALGAE
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• v.20 no.4
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• pp.261-270
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• 2005

We analyzed chloroplast ATP synthetase beta subunit(atpB) sequences from 32 strains of the zygnemophycean green algae, Staurastrum, Staurodesmus, and a single species of Xanthidium. A total of 42 atpB sequences including previously published ones was aligned for phylogenetic analyses. The phylogenies were validated with bootstrap analysis and Kishino-Hasegawa test. Taxa of Staurastrum excluding S. muticum indicate that they can be characterized by taxa having the ornamented cell wall or the process of cells. However, the genus Staurodesmus was grouped with taxa having the smooth cell wall and the absence of process or arms. The results suggest that the genus Staurodesmus could be extended to include Staurastrum muticum, Desmidium, Onychonema and Xanthidium. Further taxon sampling of Staurodesmus and putative relatives is necessary for a solid classification of the genus.

• ALGAE
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• v.33 no.1
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• pp.37-48
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• 2018

Alaria is the second largest genus of the Laminariales, which is distributed far into the northern Pacific and Atlantic oceans. Due to its high morphological plasticity, over 100 specific and sub-specific names have been used in Alaria, this has been tailored down to the present 17 species through morphological revision and molecular phylogenetic analysis. Endemic species of Alaria from Russian Far East have not been thoroughly revised since their original description, and few of them were confirmed using molecular data until recently. We carried out morphological and molecular studies on A. paradisea which is an endemic species distributed on the Kurile Islands, first described by Miyabe and Nagai in 1932 as Pleuropterum paradiseum. The range of morphological variability and its distribution was re-evaluated using the type specimen as well as other specimens. Analyses of partial mitochondrial cytochrome c oxidase subunit 1 and nuclear-encoded internal transcribed spacer sequences showed that A. paradisea nested within the genus Alaria, but differs morphologically from any other Alaria species in having additional sporophylls with a central midrib (${\beta}-sporophylls$). Our results showed that A. paradisea clearly belongs to the genus Alaria based on DNA data, although the key morphological character that was used to include this species to the genus Pleuropterum, ${\beta}-sporophylls$, is stable and distinguishes it from other Alaria species.

• Journal of Microbiology and Biotechnology
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• v.30 no.7
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• pp.1013-1017
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• 2020

Mealybugs (Hemiptera: Coccomorpha: Pseudococcidae) harbor diverse microbial symbionts that play essential roles in host physiology, ecology, and evolution. In this study we aimed to reveal microbial communities associated with two different mealybugs, papaya mealybug (Paracoccus marginatus) and two-tailed mealybug (Ferrisia virgata) collected from the same host plant. Comparative analysis of microbial communities associated with these mealybugs revealed differences that appear to stem from phylogenetic associations and different nutritional requirements. This first report on both bacterial and fungal communities associated with these mealybugs provides a preliminary insight on factors affecting the endomicrobial communities.

• Journal of Microbiology and Biotechnology
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• v.22 no.11
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• pp.1501-1509
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• 2012

A novel bacterial strain, MG7, with high cellulase activity was isolated and identified by morphological characteristics and molecular phylogeny analysis as Paenibacillus barcinonensis. Maximum production of cellulase by MG7 was observed at pH 7.0 and $35^{\circ}C$. The enzyme was purified with a specific activity of 16.88 U/mg, the cellulase activity was observed in a zymogram, and its molecular mass (58.6 kDa) was confirmed by SDS-PAGE. The purified enzyme showed maximum activity at pH 6.0 and $65^{\circ}C$ and degraded cellulosic substrates such as carboxy methyl cellulose (CMC), Avicel, filter paper, and ${\beta}$-glucan. The enzyme showed stability with 0.5% concentration of various surfactants. The $K_m$ and $V_{max}$ of cellulase for CMC and Avicel were found to be 0.459mg/ml and 10.46mg/ml/h, and 1.01 mg/ml and 10.0 mg/ml/h, respectively. The high catalytic activity and its stability to temperature, pH, surfactants, and metal ions indicated that the cellulase enzyme by MG7 is a good candidate for biotechnological applications.

• Journal of Microbiology and Biotechnology
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• v.24 no.10
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• pp.1301-1307
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• 2014

White-rot fungi of the genus Bjerkandera are cosmopolitan and have shown potential for industrial application and bioremediation. When distinguishing morphological characters are no longer present (e.g., cultures or dried specimen fragments), characterizing true sequences of Bjerkandera is crucial for accurate identification and application of the species. To build a framework for molecular identification of Bjerkandera, we carefully identified specimens of B. adusta and B. fumosa from Korea based on morphological characters, followed by sequencing the internal transcribed spacer region and 28S nuclear ribosomal large subunit. The phylogenetic analysis of Korean Bjerkandera specimens showed clear genetic differentiation between the two species. Using this phylogeny as a framework, we examined the identification accuracy of sequences available in GenBank. Analyses revealed that many Bjerkandera sequences in the database are either misidentified or unidentified. This study provides robust reference sequences for sequence-based identification of Bjerkandera, and further demonstrates the presence and dangers of incorrect sequences in GenBank.

• International Journal of Industrial Entomology and Biomaterials
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• v.15 no.2
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• pp.123-130
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• 2007

The Hsp 20.8 and Hsp 90 cDNA sequence retrieved from NCBI database and consists of 764 bp and 2582 bp lengths respectively. The corresponding cDNA homologus sequences were BLAST searched in Bombyx mori genomic DNA database and two genomic contigs viz., BAAB01120347 and AADK01011786 showed maximum homology. In B. mori Hsp 20.8 and Hsp 90 is encoded by single gene without intron. Specific primers were used to amplify the Hsp 20.8 gene and Hsp 90 variable region from genomic DNA by using the PCR. Obtained products were 216 bp in Hsp 20.8 and 437 bp in Hsp 90. There was no variation found in the six silkworm races PCR products size of contrasting response to thermal tolerance. The comparison of the sequenced nucleotide variations through multiple sequence alignment analysis of Hsp 90 variable region products of three races not showed any differences respect to their thermotolerance and formed the clusters among the voltinism. The comparison of aminoacid sequences of B. mori Hsps with dipteran and other insect taxa revealed high percentage of identity growing with phylogenetic relatedness of species. The conserved domains of B. mori Hsps predicted, in which the Hsp 20.8 possesses ${\alpha}-crystallin$ domain and Hsp 90 holds HATPase and Hsp 90 domains.