• Journal of Life Science
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• v.9 no.2
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• pp.176-181
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• 1999

In order to understand molecular phylogenetics of silkworm (Bombyx mori), we analyzed the sequences of BmoMAR isolated from Bomhyx mori that is partial coding gene of transposase of mariner-like element(MLE). By pairwise comparing nucleotide sequences of BmoMAR with ten previously reported insect MLEs accessed in GeneBank, the average genetic distance was estimated to be 0.4840. The phylogenetics tree constructed from nine insect species except for human MLE(Hsmarl) by UPGMA method indicated that MLEs are divided into three clusters, and Drosophila mariutiana was independently subgrouped. Bombyx mori(BmoMAR) was subgrouped with microcaddishfly (Orthotrichia cristata), webworm(Atteva punctella), almond moth(Ephestia cautella), Hyalopora cecropia which we lepidoptera. Phylogenetics tree according to UPGMA principle, on the basis of informative nucleotide sequences of nine insect MLEs, indicated that Bombyx mori was more closely related to microcaddishfly(Orthotrichia cristata) and webworm (Atteva punctella) of lepidoptera. We suggest that insect MLEs are a useful key for studying molecular phylogenetics among intra species of insects.

• Journal of Life Science
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• v.9 no.1
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• pp.84-89
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• 1999

To determine phylogenetic relatedness of four silk-producing silkmoths (B. mori, B. mandarina, A. yamamai and A. pernyi), internal coding region of arylphorin which is a storage protein in hemolymph protein of insects were amplified by polymerase chain reaction and then sequenced and compared each other. The nucleotide composition was biased toward adenine and thymine(59% A+T) and a strong bias for use of C in the third position of codons was found for Phe and Tyr. Together TTC(Phe) and TAC(Tyr) account for about 16.8% (10 for TTC and 8 for TAC) of all codon usage. The nucleotide similarity of arylphorin gene from B. mori showed 99%, 98% and 97% homology with those of B. mandarina, A. yamamai and A. pernyi, respectively. Also, the nucleotide sequence of arylphorin gene from B. mandarina showed 98% and 97% homology with those of A. yamamai and A.pernyi, respectively. Between A. yamamai and A. pernyi, the sequence homology was 97%. The deduced amino acid sequences in B. mori, B. mandarina and A. yamamai showed almost 99% homology. Although the aryphorin gene provided insufficient variability among the four insect species, A UPGMA tree is generated that supported the monophyly of silk-producing insects, with M. sexta placed basal to it. It is suggest that silk-producing insects have a close relationship and a homogeneous genetic background from comparison with those of other insects.

• Journal of Microbiology and Biotechnology
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• v.12 no.1
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• pp.130-136
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• 2002

The internal transcribed spacer (ITS) region in the genus Tricholoma was analyzed, including for its primary nucleotide sequence and secondary structural characterization. The secondary structures of the ITS2 region in the genus Tricholoma were identified for use in bioinformatic processes to study molecular evolution and compare secondary structures. Ten newly sequenced ITS regions were added to the analysis and submitted to the GenBank database. The resulting structure from a minimum energy algorithm indicated the four-domain model, as previously suggested by others. The conserved secondary structure of the ITS2 sequences of the genus Tricholoma exhibited certain unique features, including pyrimidine tracts in the loops of domain A and a complete structure containing four domains, with motifs identified in other ITS2 secondary structures. A phylogenetic tree was derived from sequence alignment based on the secondary structures. From the resulting maximum parsimonious tree, it was found that the species in the genus Tricholoma had evolved monophyletically and were composed of four groups, as supported by the bootstrapping values and pileus color.

• Parasites, Hosts and Diseases
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• v.55 no.1
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• pp.31-37
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• 2017

This study aimed to investigate the morphology and reconstruct the phylogenetic relationships of Centrocestus formosanus originating from 5 species of freshwater fish, i.e., Esomus metallicus, Puntius brevis, Anabas testudineus, Parambassis siamensis, and Carassius auratus, in Chiang Mai province, Thailand. Sequence-related amplified polymorphism (SRAP) and phylogeny based on internal transcribed spacer 2 (ITS2) and mitochondrial cytochrome c oxidase subunit 1 (CO1) were performed. The results showed similar morphologies of adult C. formosanus from day 5 after infection in chicks. C. formosanus originated from 4 species of freshwater fish had the same number of circumoral spines on the oral sucker, except for those from C. auratus which revealed 34 circumoral spines. The phylogenetic tree obtained from SRAP profile and the combination of ITS2 and CO1 sequence showed similar results that were correlated with the number of circumoral spines in adult worms. Genetic variability of C. formosanus also occurred in different species of freshwater fish hosts. However, more details of adult worm morphologies and more sensitive genetic markers are needed to confirm the species validity of C. formosanus with 34 circumoral spines originating from C. auratus in the future.

• Parasites, Hosts and Diseases
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• v.54 no.6
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• pp.813-817
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• 2016

Armillifer agkistrodontis (Ichthyostraca: Pantastomida) is a parasitic pathogen, only reported in China, which can cause a zoonotic disease, pentastomiasis. A complete mitochondrial (mt) genome was 16,521 bp comprising 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and 1 non-coding region (NCR). A phylogenetic tree drawn with the concatenated amino acid sequences of the 6 conserved PCGs (atp6, cox1-3, and nad2) showed that A. agkistrodontis and Armillifer armillatus constituted a clade Pentastomida which was a sister group of the Branchiura. The complete mt genome sequence of A. agkistrodontis provides important genetic markers for both phylogenetic and epidemiological studies of pentastomids.

• Journal of Species Research
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• v.8 no.3
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• pp.313-317
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• 2019

Bats influence overall ecosystem health by regulating species diversity and being a major source of zoonotic viruses. Hence, there is a need to elucidate their migration, population structure, and phylogenetic relationship. The complete mitochondrial genome is widely used for studying the genome-level characteristics and phylogenetic relationship of various animals due to its high mutation rate, simple structure, and maternal inheritance. In this study, we determined the complete mitogenome sequence of the bird-like noctule (Nyctalus aviator) by Illumina next-generation sequencing. The sequences obtained were used to reconstruct a phylogenic tree of Vespertilionidae to elucidate the phylogenetic relationship among its members. The mitogenome of N. aviator is 16,863-bp long with a typical vertebrate gene arrangement, consisting of 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 putative control region. Overall, the nucleotide composition is as follows: 32.3% A, 24.2% C, 14.3% G, and 29.2% T, with a slight AT bias (61.5%). The base composition of the 13 PCGs is as follows: 30.3% A, 13.4% G, 31.0% T, and 25.2% C. The phylogenetic analysis, based on 13 concatenated PCG sequences, infers that N. aviator is closely related to N. noctula with a high bootstrap value (100%).

• Korean Journal of Microbiology
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• v.47 no.3
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• pp.268-274
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• 2011

Anabaena (Cyanobacteria, Nostocales) are important for water quality controls, because they are often responsible for freshwater green tides; moreover, some species are reported to produce hepatotoxin. In this study, we sequenced RNA polymerase beta subunit (rpoB) gene of Anabaena, and evaluated their sequences for the potential use of a molecular taxonomic marker in this taxon. Anabaena rpoB showed low DNA similarity and high genetic divergences when compared those of 16S rRNA, and the molecular differences were statistically significant (Student t-test, p<0.01). Parsimony analyses showed the rpoB gene evolves 4.8-fold faster than 16S rRNA. In addition, phylogeny of the rpoB gene separated each Anabaena strain more clearly compared with a 16S rRNA tree. These results suggest that the rpoB gene is a useful marker for the molecular phylogenetics and the species discrimination of Anabaena.

• Korean Journal of Microbiology
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• v.46 no.3
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• pp.296-302
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• 2010

Microcystis (Cyanobacteria, Chroococcales) is one of the green tide-causing organisms in freshwaters, and some species produce microcystin that is hepatotoxin. In the aspects of freshwater quality controls and health concerns, therefore it is necessary to manage the harmful organisms. In the present study, RNA polymerase beta subunit (rpoB) gene sequences of Microcystis were determined and characterized in order to use a potential marker for the molecular detections of the species. Microcystis rpoB showed high divergences of DNA similarity and genetic distances when compared with those of 16S rRNA, and the molecular differences were statistically significant (Student t-test, p<0.05). Parsimony analyses showed the rpoB gene evolves more than 2-fold faster than 16S rRNA. In addition, phylogeny of the rpoB gene separated each M. aeruginosa strain more clearly compared with a 16S rRNA tree. This study found that the order Chroococcales, including Microcystis, has approximately two rRNA operons and single copy of the rpoB gene in their chromosomes. These results suggest that the rpoB gene is a useful marker for the molecular phylogenetics and the detection of Microcystis.

• Korean Journal of Ichthyology
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• v.33 no.4
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• pp.205-216
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• 2021

Phylogenetic reconstruction based on one locus or a few loci can be misleading due to gene-tree/species-tree discordance. Species delimitation and intraspecific studies also often suffered from low resolution because of insufficient statistic power when few loci were used. Exon capture method is one of the most efficient way to collect genome-scale data, which can significantly augment studies that aimed to investigate patterns and histories of organisms at both intraspecific and high level. Here, I showed the advancement of shifting from single-gene method to genomic approach and the benefit of applying exon capture method comparing to alternative genomic techniques. Then, I explained the principle of exon capture method as well as providing detailed recommendations for applying this method. Finally, I demonstrated exon capture method using two applications and discussed future perspectives of this technology.