• Animal Systematics, Evolution and Diversity
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• v.39 no.3
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• pp.99-113
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• 2023

The nudibranch is one of the most colorful gastropod species found in oceans worldwide. Unlike many other gastropod groups, the nudibranch loses an external shell in the adult stage, but instead develops various chemical defense systems. More than 2,500 nudibranch species have been reported worldwide, and 73 species are currently recorded in Korean waters. In this study, we present morphological descriptions, DNA barcode information of mtDNA cox1 sequence, and taxonomic review for five nudibranch species: Apata pricei (MacFarland, 1966), Doto rosacea Baba, 1949, Janolus toyamensis Baba and Abe, 1970, Polycera abei (Baba, 1960), and Trinchesia sibogae (Bergh, 1905). Of these, we also provide in-depth discussion of taxonomic issue of A. pricei that was previously subdivided into two subspecies, A. pricei pricei and A. pricei komandorica. Our morphological examination and molecular analyses of the mtDNA cox1 sequences indicate that these two subspecies are not taxonomically warranted. The phylogenetic information for the other nudibranch species from mtDNA cox1 sequence analysis is also included, providing a molecular basis for species identification and inferring their local phylogenies within each of the species groups discussed herein.

• Animal Systematics, Evolution and Diversity
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• v.40 no.2
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• pp.130-134
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• 2024

The family Velutinidae is found in various intertidal and subtidal habitats worldwide including Arctic and Antarctic seas. They are characterized by possessing a fragile shell that is partially or entirely covered by the mantle. Eight valid species of the genus Coriocella have been reported mostly in the Indo-West Pacific. Here we report Coriocella jayi Wellens, 1996 from Korean waters for the first time and describe details of their external morphology and radula characteristics using scanning electron microscopy, and provide the mtDNA cox1 sequence as a DNA barcode sequence information. This species is distinguished from other congeneric species by having six cylinder-shaped tubercular lobes of their dorsal part of mantle body and mantle color. Phylogenetic tree using the mtDNA cox1 sequence data shows that two Coriocella species (C. jayi and C. nigra) are grouped as their respective sister among Velutinidae species, and these relationships are strongly supported by 100% bootstrap value. Despite the morphological similarities, further investigation will be needed to confirm whether the African and Korean populations can be justified as the same species with a disconnected distribution range, or represent morphologically similar but two distinct species.

• Journal of Species Research
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• v.11 no.2
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• pp.102-107
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• 2022

The order Nudibranchia Cuvier, 1817 is among the most colorful gastropod group that lacks an external shell and mantle cavity at their adult stage. They are widely found in the intertidal to subtidal zones of marine habitats worldwide. To date, a total of 58 species are known from Korean waters. In this study, we report seven nudibranch species that are newly reported from Korean waters and provide their color images of external body, morphological description, taxonomic remarks, and mtDNA cox1 barcode sequence information: Dendronotus primorjensis Martynov, Sanamyan & Korshunova, 2015; Doto japonica Odhner, 1936; Trinchesia ornata (Baba, 1937); Antiopella fusca (O'Donoghue, 1924); Cadlina paninae Korshunova, Fletcher, Picton, Lundin, Kashio, N. Sanamyan, K. Sanamyan, Padula, Schrodi & Martynov, 2020; Rostanga bifurcata Rudman & Avern, 1989; and Goniodoridella savignyi Pruvot-Fol, 1933.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.44 no.3
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• pp.243-247
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• 1999

Mitochondrial DNA restriction fragment length polymorphisms are convenient markers for identifying cytoplasmic variation among plants. We have collected 212 wild soybeans (Glycine soja Sieb. et Zucc) from all over Korea, and classified mitochondrial genome types based on hybridization patterns in DNA gel-blot analyses using two mitochondrial DNA clones, cox2 and atp6, as probes. Korean wild soybean was classified with eight-mtDNA types, and some of the mtDNAs showed geographical clines among the regions. The diversity index of the mtDNA was much higher in the western and southern regions than in the eastern and northern regions of Korea, respectively. Dissemination and distributive characteristics of wild soybeans in Korea were discussed.

• Parasites, Hosts and Diseases
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• v.52 no.1
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• pp.9-19
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• 2014

Anisakis spp. (Nematoda: Anisakidae) parasitize a wide range of marine animals, mammals serving as the definitive host and different fish species as intermediate or paratenic hosts. In this study, 18 fish species were investigated for Anisakis infection. Katsuwonus pelamis, Euthynnus affinis, Caranx sp., and Auxis thazard were infected with high prevalence of Anisakis type I, while Cephalopholis cyanostigma and Rastrelliger kanagurta revealed low prevalence. The mean intensity of Anisakis larvae in K. pelamis and A. thazard was 49.7 and 5.6, respectively. A total of 73 Anisakis type I larvae collected from K. pelamis and A. thazard were all identified as Anisakis typica by PCR-RFLP analysis. Five specimens of Anisakis from K. pelamis and 15 specimens from A. thazard were sequenced using ITS1-5.8S-ITS2 region and 6 specimens from A. thazard and 4 specimens from K. pelamis were sequenced in mtDNA cox2 region. Alignments of the samples in the ITS region showed 2 patterns of nucleotides. The first pattern (genotype) of Anisakis from A. thazard had 100% similarity with adult A. typica from dolphins from USA, whereas the second genotype from A. thazard and K. pelamis had 4 base pairs different in ITS1 region with adult A. typica from USA. In the mtDNA cox2 regions, Anisakis type I specimens from A. thazard and K. pelamis showed similarity range from 94% to 99% with A. typica AB517571/DQ116427. The difference of 4 bp nucleotides in ITS1 regions and divergence into 2 subgroups in mtDNA cox2 indicating the existence of A. typica sibling species in the Makassar Strait.

• 한국균학회소식:학술대회논문집
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• 2015.11a
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• pp.41-41
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• 2015

Oomycetes belong to the kingdom Straminipila, a remarkably diverse group which includes brown algae and planktonic diatoms, although they have previously been classified under the kingdom Fungi. These organisms have evolved both saprophytic and pathogenic lifestyles, and more than 60% of the known species are pathogens on plants, the majority of which are classified into the order Peronosporales (includes downy mildews, Phytophthora, and Pythium). Recent phylogenetic investigations based on DNA sequences have revealed that the diversity of oomycetes has been largely underestimated. Although morphology is the most valuable criterion for their identification and diversity, morphological species identification is time-consuming and in some groups very difficult, especially for non-taxonomists. DNA barcoding is a fast and reliable tool for identification of species, enabling us to unravel the diversity and distribution of oomycetes. Accurate species determination of plant pathogens is a prerequisite for their control and quarantine, and further for assessing their potential threat to crops. The mitochondrial cox2 gene has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA. To determine which out of cox1 or cox2 is best suited as universal oomycete barcode, we compared these two genes in terms of (1) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (2) in terms of sequence polymorphism, intra- and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three genera. In addition, cox2 exhibited higher PCR efficiency for historic herbarium specimens, providing easier access to barcoding type material. In addition, cox2 yielded higher species identification success, with higher interspecific and lower intraspecific divergences than cox1. Therefore, cox2 is suggested as a partner DNA barcode along with ITS rDNA instead of cox1. Including the two barcoding markers, ITS rDNA and cox2 mtDNA, the multi-locus phylogenetic analyses were performed to resolve two complex clades, Bremia lactucae (lettuce downy mildew) and Peronospora effuse (spinach downy mildew) at the species level and to infer evolutionary relationships within them. The approaches discriminated all currently accepted species and revealed several previously unrecognized lineages, which are specific to a host genus or species. The sequence polymorphisms were useful to develop a real-time quantitative PCR (qPCR) assay for detection of airborne inoculum of B. lactucae and P. effusa. Specificity tests revealed that the qPCR assay is specific for detection of each species. This assay is sensitive, enabling detection of very low levels of inoculum that may be present in the field. Early detection of the pathogen, coupled with knowledge of other factors that favor downy mildew outbreaks, may enable disease forecasting for judicious timing of fungicide applications.

• Parasites, Hosts and Diseases
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• v.57 no.1
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• pp.55-60
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• 2019

This study was undertaken to determine the complete mitochondrial DNA sequence and structure of the mitochondrial genome of Spirometra ranarum, and to compare it with those of S. erinaceieuropaei and S. decipiens. The aim of this study was to provide information of the species level taxonomy of Spirometra spp. using the mitochondrial genomes of 3 Spirometra tapeworms. The S. ranarum isolate originated from Myanmar. The mitochondrial genome sequence of S. ranarum was compared with that of S. erinaceieuropaei (GenBank no. KJ599680) and S. decipiens (GenBank no. KJ599679). The complete mtDNA sequence of S. ranarum comprised 13,644 bp. The S. ranarum mt genome contained 36 genes comprising 12 protein-coding genes, 22 tRNAs and 2 rRNAs. The mt genome lacked the atp8 gene, as found for other cestodes. All genes in the S. ranarum mitochondrial genome are transcribed in the same direction and arranged in the same relative position with respect to gene loci as found for S. erinaceieuropaei and S. decipiens mt genomes. The overall nucleotide sequence divergence of 12 protein-coding genes between S. ranarum and S. decipiens differed by 1.5%, and 100% sequence similarity was found in the cox2 and nad6 genes, while the DNA sequence divergence of the cox1, nad1, and nad4 genes of S. ranarum and S. decipiens was 2.2%, 2.1%, and 2.6%, respectively.

• ALGAE
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• v.33 no.1
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• pp.49-54
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• 2018

Red algal mitochondrial genomes (mtDNAs) can provide useful information on species identification. mtDNAs of Pyropia / Porphyra (Bangiales, Rhodophyta) have shown diverse variation in their size and gene structure. In particular, the introns and intronic open reading frames found in the ribosomal RNA large subunit gene (rnl) and cytochrome c oxidase subunit 1 gene (cox1) significantly vary the mitochondrial genome size in Pyropia / Porphyra species. In this study, we examined the exon / intron structure of rnl and cox1 genes of Pyropia yezoensis at the intraspecific level. The combined data of rnl and cox1 genes exhibited 12 genotypes for 40 P. yezoensis strains, based on the existence of introns. These genotypes were more effective to identify P. yezoensis strains in comparison to the traditional DNA barcode cox1 marker (5 haplotypes). Therefore, the variation in gene structure of rnl and cox1 can be a novel molecular marker to discriminate the strains of Pyropia species.

• Journal of fish pathology
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• v.33 no.1
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• pp.15-21
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• 2020

We found skin flukes in snubnose pompano (Trachinotus blochii) from a public aquarium and attempted clear identification of them to the species level by morphology and molecular analyses. Skin flukes were collected from snubnose pompano showing dyspnea, anorexia and mild hemorrhage on the skin. All the fish samples (n=2) were infected with the flukes on the skin, gill and eyes, covered with excessive mucus. The isolated worms were transferred for making slide specimen and PCR amplification targeting 18S rDNA, 28S rDNA, mitochondrial cytochrome c oxidase subunit 1 (mt cox1) and cytochrome b (Cytb) genes for further analyses. Morphology and measurements data of our slide specimen coincided with those of Neobenedenia girellae. The sequence data of 2 genes (28S rDNA and Cytb) and the phylogenetic trees revealed that our specimen consistently belonged to the N. girellae clade. For 18S rDNA and mt cox1 genes, there was no sequence of either of these 2 Neobenedenia species from the type host available in GenBank. This is the first record of N. girellae in snubnose pompano, but it is still unclear if the snubnose pompano is a natural host for N. girellae or not because N. girellae is known to have an unusual broad host range and the host-switching can occur particularly in captive conditions such as aquarium or aquaculture facilities.

• Parasites, Hosts and Diseases
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• v.49 no.4
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• pp.399-403
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• 2011

Species identification of Taenia tapeworms was performed using morphologic observations and multiplex PCR and DNA sequencing of the mitochondrial cox1 gene. In 2008 and 2009, a total of 1,057 fecal samples were collected from residents of Kongwa district of Dodoma region, Tanzania, and examined microscopically for helminth eggs and proglottids. Of these, 4 Taenia egg positive cases were identified, and the eggs were subjected to DNA analysis. Several proglottids of Taenia solium were recovered from 1 of the 4 cases. This established that the species were T. solium (n=1) and T. saginata (n=3). One further T. solium specimen was found among 128 fecal samples collected from Mbulu district in Arusha, and this had an intact strobila with the scolex. Phylegenetic analysis of the mtDNA cox1 gene sequences of these 5 isolates showed that T. saginata was basal to the T. solium clade. The mitochondrial cox1 gene sequences of 3 of these Tanzanian isolates showed 99% similarity to T. saginata, and the other 2 isolates showed 100% similarity to T. solium. The present study has shown that Taenia tapeworms are endemic in Kongwa district of Tanzania, as well as in a Previously identified Mbulu district. Both T. solium isolates were found to have an "African/Latin American" genotype (cox1).