• Parasites, Hosts and Diseases
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• v.60 no.4
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• pp.273-279
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• 2022

Laelapinae mites are involved in transmission of microbial diseases between wildlife and humans, with an impact on public health. In this study, 5 mite members in the subfamily Laelapinae (laelapin mites; LM) were morphologically identified by light microscopy, and the phylogenetic relationship of LM was analyzed in combination with the sequence information of part of the LM cytochrome oxidase subunit I (cox1) gene. The morphological identification revealed that 5 mites belonged to the genera Laelaps and Haemolaelaps, respectively. Sequence analysis showed that the ratio of nonsynonymous mutation rate to synonymous mutation rate of LM was less than 1, indicating that the LM cox1 gene had undergone purifying selection. Phylogenetic analysis showed that the Laelapinae is a monophyletic group. The genera Haemolaelaps and Hyperlaelaps did not separated into distinct clades but clustered together with species of the genus Laelaps. Our morphological and molecular analyses to describe the phylogenetic relationships among different genera and species of Laelapinae provide a reference for the improvement and revision of the LM taxonomy system.

• 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.

• Korean Journal of Veterinary Service
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• v.39 no.1
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• pp.1-6
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• 2016

In this study, Bacillus licheniformis which has been used as probiotics was isolated from Korean traditional fermented soybean. A total of 69 strains were presumptively identified as B. licheniformis by phenotypic methods. Based on PCR amplification and 16S rRNA gene sequencing, the multilocus sequence typing of gyrA and rpoB, followed by phylogenetic analysis was performed. The isolates were distinctly differentiated and found to be closely related to B. amyloliquefaciens, B. subtilis, and B. aerius. The partial 16S rRNA gene sequences of those strains matched those of B. sonorensis (97%) and B. aerius (98%) in the phylogenetic tree. In contrast, multilocus phylogenetic analysis (MLPA) showed that only 61 (86.9%) out of 69 strains were B. licheniformis. The rest of those strains were found to be B. subtilis (5.8%), B. amyloliquefaciens (2.9%), and B. sonorensis (2.9%), respectively. Therefore, our results suggested that since the 16S rRNA gene sequencing alone was not sufficient to compare and discriminate closely related lineages of Bacillus spp., it was required to analyze the MLPA simultaneously to avoid any misleading phenotype-based grouping of these closely related species.

• The Korean Journal of Mycology
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• v.47 no.2
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• pp.95-104
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• 2019

The genus Ochrolechia is a widespread, lichen genus in Korea. Despite being common, little is known about the species diversity and geographical distribution of Ochrolechia. In this study, we detailed the identification procedure of the genus Ochrolechia in a Korean collection and provided the description of each species. Using 104 specimens collected from 2003 to 2017, we identified four species of the genus Ochrolechia via morphological and/or molecular phylogenetic analysis: O. parellula, O. trochophora, O. yasudae and O. akagiensis. Among them, O. akagiensis had not been previously reported in Korea. Moreover, the species identified as O. frigida and O. tartarea in past studies were corrected as O. yasudae and O. parellula, respectively, based on morphological and/or molecular evidence. Phylogenetic analysis using the internal transcribed spacer regions including 5.8S rRNA gene showed that the four species separated clearly, indicating that the morphological identification corresponds to the phylogenetic identification. We provide a taxonomic key for the four species of the genus Ochrolechia.

• Proceedings of the National Institute of Ecology of the Republic of Korea
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• v.3 no.4
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• pp.212-220
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• 2022

DNA markers have been studied and used intensively to identify plant species based on molecular approaches. The genus Medicago belongs to the family Fabaceae and contains 87 species distributed from the Mediterranean to central Asia. Five species of Medicago are known to be distributed in South Korea; however, their morphological characteristics alone cannot distinguish the species. In this study, we analyzed the phylogenetic relationships using collected five species of Medicago from South Korea and 44 taxa nucleotide information from NCBI. The constructed phylogenetic tree using gibberellin 3-oxidase 1 and tRNA^Lys (UUU) to maturase K gene sequences showed the monophyly of the genus Medicago, with five species each forming a single clade. These results suggest that there are five species of Medicago distributed in South Korea. In addition, we designed polymerase chain reaction primers for species-specific detection of Medicago by comparing the plastid sequences. The accuracy of the designed primer pairs was confirmed for each Medicago species. The findings of this study provide efficient and novel species identification methods for Medicago, which will assist in the identification of wild plants for the management of alien species and living modified organisms.

• Journal of fish pathology
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• v.22 no.3
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• pp.391-400
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• 2009

Genetic identification of 17 fish-derived Aeromonas strains was attempted using 5 housekeeping genes. 16S rRNA, gyrB, rpoD, dnaJ and recA genes from the 17 strains were amplified, and total of 85 amplicons were sequenced. DNA sequences of the strains and type strains of the 17 Aeromonas homology groups were used for genetic identification and phylogenetic analyses. None of the strains was identified as a single species using the 16S rRNA gene, showing the same identities (average = 99.7%) with several Aeromonas species. According to gyrB, rpoD, dnaJ, and recA, 9 strains and RFAS-1 used in this study were identified as A. hydrophila and A. salmonicida, respectively. However, the other strains were closely related to 2 or more Aeromonas species (i.e., A. salmonicida, A. veronii, A. jandaei, A. media and A. troda) depending on the genetic marker used. In this study, gyrB, rpoD, dnaJ and recA gene sequences proved to be advantageous over 16S rRNA for the identification of field Aeromonas isolates obtained from fish. However, there are discrepancies between analyses of different phylogenetic markers, indicating there are still difficulties in genetic identification of the genus Aeromonas using the housekeeping genes used in this study. Advantages and disadvantages of each housekeeping gene should be taken into account when the gene is used for identification of Aeromonas species.

• Animal Systematics, Evolution and Diversity
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• v.29 no.4
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• pp.272-278
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• 2013

Accurate identification of fish and fish products, from eggs to adults, is important in many areas. Grey mullets of the family Mugilidae are distributed worldwide and inhabit marine, estuarine, and freshwater environments in all tropical and temperate regions. Various Mugilid species are commercially important species in fishery and aquaculture of many countries. For the present study we have chosen two Mugilid genes with different phylogenetic signals: relatively variable mitochondrial cytochrome oxidase subunit I (COI) and conservative nuclear rhodopsin (RHO). We examined their diversity within and among 9 Mugilid species belonging to 4 genera, many of which have been examined from multiple specimens, with the goal of determining whether DNA barcoding can achieve unambiguous species recognition of Mugilid species. The data obtained showed that information based on COI sequences was diagnostic not only for species-level identification but also for recognition of intraspecific units, e.g., allopatric populations of circumtropical Mugil cephalus, or even native and acclimatized specimens of Chelon haematocheila. All RHO sequences appeared strictly species specific. Based on the data obtained, we conclude that COI, as well as RHO sequencing can be used to unambiguously identify fish species. Topologies of phylogeny based on RHO and COI sequences coincided with each other, while together they had a good phylogenetic signal.

• Journal of Microbiology and Biotechnology
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• v.14 no.4
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• pp.816-821
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• 2004

A reliable molecular phylogenetic method to identify Hericium erinaceum, the most industrially valuable species in the Hericium genus, was established. Sequencing and phylogenetic analyses of the PCR-amplified ITS and 5.8S rDNA from Hericium fungi, including 6 species and 23 isolates, showed that variation in nucleotide sequences and size exists in both ITS1 and ITS2 regions, but not in the 5.8S region. These two ITS regions provided different levels of information on the relationship of H. erinaceum to other Hericium species. Based on the ITS1 sequence, both the parsimony and neighbor joining trees clearly distinguished Asian H. erinaceum isolates from other Hericium species and isolates. The intraspecific divergence of the ITS2 region was suitable to dissect the Asian H. erinaceum isolates into a few groups.

• Mycobiology
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• v.50 no.2
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• pp.150-154
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• 2022

Rhytisma lonicericola was identified as a tar spot fungus on Lonicera sp. in 1902, and has since been recorded on several species of Lonicera in China, Japan, and Korea. Most of the previous records of R. lonicericola have been based on a list of disease occurrences in the absence of any formal morphological identification or molecular analyses. Using six newly obtained specimens collected in the past 2 years, we confirmed the tar spot fungus found on L. japonica in Korea as R. lonicericola based on morphological examinations and molecular phylogenetic analyses. This fungus was distinguished from R. xylostei, another tar spot fungus on Lonicera, by ascospore size and geographical distributions. We present detailed mycological information and, for the first time, DNA sequence data useful for the identification of R. lonicericola.

• Journal of fish pathology
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• v.35 no.1
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• pp.135-140
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• 2022

In this study, we determined the cause of a disease outbreak in small yellow croaker(Larimichthys polyactis) in Jeju island. The major external signs in the dead fish were hemorrhage of the skin. Vibrio harveyi were isolated from a few fishes and viruses were not detected from the diseased fish. However, flukes were confirmed on the skin and we conducted molecular identification and phylogenetic analysis of the isolated parasites. The obtained 28S rRNA sequence of our specimen(Accession No. OM333244) showed the highest homology with Neobenedenia girellae, while the COI sequence of our specimen showed the highest homology with N. melleni. Further sequence analysis with other genes and morphological observation are necessary for accurate identification.