Joong-Ki Park

Korea Polar Research Institute, Sŏul, Seoul, South Korea

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Publications (37)67.03 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Abstract Slipper lobsters are a unique group of decapod crustaceans; they have cylindrical or flattened bodies and belong to the family Scyllaridae. The genus Ibacus (Leach, 1815) (Achelata, Scyllaridae, Ibacinae) consists of eight recognized species to date, all of which occur in the Indo-West Pacific Ocean and are commercially important seafood species. The complete mitochondrial genome of the Japanese fan lobster Ibacus ciliatus (Von Siebold, 1824) is 15,696 bp in size and consists of 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a control region of 783 bp. The base composition of I. ciliatus is 35.8% A, 34.7% T, 19.0% C, and 10.5% G, with an overall AT content of 70.5%. The mitogenome of I. ciliatus was found to have gene arrangement and transcriptional polarity identical to that of the American lobster Homarus americanus, showing the pancrustacean ground pattern. Here, we present the complete mitogenome sequence of I. ciliatus; it is the first mitogenome information from the subfamily Ibacinae, and represents the second for the family Scyllaridae.
    Mitochondrial DNA 10/2014; · 1.71 Impact Factor
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    ABSTRACT: Abstract The violet-spotted reef lobster Enoplometopus debelius Holthuis, 1983 (Decapoda, Astacidea, Enoplometopidae) is found in the tropical reef areas of the Indo-Pacific region, and is a highly prized and very popular species in the aquarium trade industry. The complete mitochondrial genome of E. debelius has 15,641 base pairs consisting of 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a control region of 746 bp. The base composition of E. debelius is 36.4% A, 35.3% T, 18.1% C, 10.3% G, and the species has an AT content of 71.7%. The E. debelius mitogenome was found to have a gene arrangement and transcriptional polarity identical to that of the Homarus americanus mitogenome, a representative of the arthropod ground pattern. Here, we present the complete mitogenome sequence of E. debelius, which is the first in the superfamily Enoplometopoidea. These data will provide a useful molecular resource for the phylogenetic study of the infraorder Astacidea/order Decapoda.
    Mitochondrial DNA 09/2014; · 1.71 Impact Factor
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    Sang-Hwa Lee, Joong-Ki Park
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    ABSTRACT: The Conus Linnaeus, 1758 is a large genus of marine gastropod mollusks belonging to the family Conidae. The Conus species are mostly distributed in the tropical waters of the world, and they are especially abundant in the Indo-West Pacific region. To date, more than 600 species, most of which are predatory species, have been named worldwide in this genus and only six species have been recorded in the Korean waters. Conus sponsalis Hwass in Bruguire, 1792 was collected from Jeju Island and identified as a new Korean record. In this study, we report a description of the shell morphology of the species.
    Animal Systematics, Evolution and Diversity. 01/2014; 30(1).
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    ABSTRACT: The complete mitochondrial genome was sequenced and annotated newly from an individual of Crocidura shantungensis (Soricidae) from Korea. The total length of the C. shantungensis genome is 17,160 bp, with a base composition of 32.5% A, 32.7% T, 21.6% C, and 13.1% G.
    Mitochondrial DNA 06/2013; 24(3):202-204. · 1.71 Impact Factor
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  • Tahera Sultana, Hyerim Han, Joong-Ki Park
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    ABSTRACT: We determined the complete mitochondrial genome sequences for Bursaphelenchus mucronatus, one species of pinewood nematode. The genome is a circular-DNA molecule of 14,583bp (195bp smaller than its congener Bursaphelenchus xylophilus) and contains 12 protein-coding genes (lacking atp8), 22 tRNA genes, and 2 rRNA genes encoded in the same direction, consistent with most other nematodes. Based on sequence comparison of mtDNA genomes, we developed a PCR-based molecular assay to differentiate B. xylophilus (highly pathogenic) and B. mucronatus (relatively less virulent) using species-specific primers. The molecular identification system employs multiplex-PCR and is very effective and reliable for discriminating these Bursaphelenchus species, which are economically important, but difficult to distinguish based on morphology. The comparison of the mitochondrial genomes and molecular identification system of the two species of Bursaphelenchus spp. should provide a rich source of genetic information to support the effective control and management (quarantine) of the pine wilt disease caused by pinewood nematodes.
    Gene 02/2013; · 2.20 Impact Factor
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    ABSTRACT: We determined the complete mitochondrial (mt) genome sequence of the red king crab, Paralithodes camtschaticus (Decapoda, Anomura). P. camtschaticus is one of the largest arthropods and the most expensive commercially available gourmet seafood. The genome sequence of P. camtschaticus is 16,720 bp in size and its gene content, gene order, and transcriptional polarity are almost identical to those of the hermit crab Pagurus longicarpus, which is thought to be derived from a common ancestor. However, P. camtschaticus mtDNA showed tRNA translocation in two blocks compared to that of P. longicarpus. Prior to this study, complete mt genomes of only two species of Anomura have been reported. Thus, our genomic data will provide additional information for constructing the decapod phylogeny.
    Mitochondrial DNA 01/2013; · 1.71 Impact Factor
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    ABSTRACT: BACKGROUND: The nematode infraorder Tylenchomorpha (Class Chromadorea) includes plant parasites that are of agricultural and economic importance, as well as insect-associates and fungal feeding species. Among tylenchomorph plant parasites, members of the superfamily Tylenchoidea, such as root-knot nematodes, have great impact on agriculture. Of the five superfamilies within Tylenchomorpha, one (Aphelenchoidea) includes mainly fungal-feeding species, but also some damaging plant pathogens, including certain Bursaphelenchus spp. The evolutionary relationships of tylenchoid and aphelenchoid nematodes have been disputed based on classical morphological features and molecular data. For example, similarities in the structure of the stomatostylet suggested a common evolutionary origin. In contrast, phylogenetic hypotheses based on nuclear SSU ribosomal DNA sequences have revealed paraphyly of Aphelenchoidea, with, for example, fungal-feeding Aphelenchus spp. within Tylenchomorpha, but Bursaphelenchus and Aphelenchoides spp. more closely related to infraorder Panagrolaimomorpha. We investigated phylogenetic relationships of plant-parasitic tylenchoid and aphelenchoid species in the context of other chromadorean nematodes based on comparative analysis of complete mitochondrial genome data, including two newly sequenced genomes from Bursaphelenchus xylophilus (Aphelenchoidea) and Pratylenchus vulnus (Tylenchoidea). RESULTS: The complete mitochondrial genomes of B. xylophilus and P. vulnus are 14,778 bp and 21,656 bp, respectively, and identical to all other chromadorean nematode mtDNAs in that they contain 36 genes (lacking atp8) encoded in the same direction. Their mitochondrial protein-coding genes are biased toward use of amino acids encoded by T-rich codons, resulting in high A+T richness. Phylogenetic analyses of both nucleotide and amino acid sequence datasets using maximum likelihood and Bayesian methods did not support B. xylophilus as most closely related to Tylenchomorpha (Tylenchoidea). Instead, B. xylophilus, was nested within a strongly supported clade consisting of species from infraorders Rhabditomorpha, Panagrolaimomorpha, Diplogasteromorpha, and Ascaridomorpha. The clade containing sampled Tylenchoidea (P. vulnus, H. glycines, and R. similis) was sister to all analyzed chromadoreans. Comparison of gene arrangement data was also consistent with the phylogenetic relationships as inferred from sequence data. Alternative tree topologies depicting a monophyletic grouping of B. xylophilus (Aphelenchoidea) plus Tylenchoidea, Tylenchoidea plus Diplogasteromorpha (Pristionchus pacificus), or B. xylophilus plus Diplogasteromorpha were significantly worse interpretations of the mtDNA data. CONCLUSIONS: Phylogenetic trees inferred from nucleotide and amino acid sequences of mtDNA coding genes are in agreement that B. xylophilus (the single representative of Aphelenchoidea) is not closely related to Tylenchoidea, indicating that these two groups of plant parasites do not share an exclusive most recent common ancestor, and that certain morphological similarities between these stylet-bearing nematodes must result from convergent evolution. In addition, the exceptionally large mtDNA genome size of P. vulnus, which is the largest among chromadorean nematode mtDNAs sequenced to date, results from lengthy repeated segments in non-coding regions.
    BMC Evolutionary Biology 01/2013; 13(1):12. · 3.29 Impact Factor
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    ABSTRACT: We determined the complete mitochondrial (mt) genome sequence of the Japanese ghost shrimp Nihonotrypaea japonica (Ortmann 1891) (Crustacea, Decapoda, Axiidea). The N. japonica mt genome is first represented in infraorder Axiidea, which, together with infraorder Gebiidea, belonged to infraorder Thalassinidea until recently. The genome sequence of N. japonica is 15,274 bp in size, and the gene arrangement and transcriptional polarity are partially different from that of the Japanese mud shrimp, Upogebia major, which belongs to the infraorder Gebiidea. We present the mt genome of N. japonica, which could provide useful molecular information to construct a stable classification for infraorder Thalassinidea and to better understand the phylogenetic relationship of Thalassinidea with other decapod groups.
    Mitochondrial DNA 01/2013; · 1.71 Impact Factor
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    Junhee Lee, Sang-Hwa Lee, Joong-Ki Park
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    ABSTRACT: The Strombus Linn, 1758 is a genus of marine mollusks belonging to the class Gastropoda, and is distributed in the tropical waters of the world. Typically, the family Strombidae includes five extant genera (Strombus, Lambis, Terebellum, Tibia, and Rimella), all of which are mostly found in tropical waters. Five individuals of Strombus luhuanus Linn, 1758 were collected from Uljin, Gyeongsangbuk-do province for the first time. In this study, we describe details of shell morphology and radula characters of the species with scanning electron microscopy images of the radula. This is a new record of Strombus luhuanus Linn, 1758 from Korean waters.
    Animal Systematics, Evolution and Diversity. 01/2013; 29(1).
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    Sang-Hwa Lee, Joong-Ki Park
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    ABSTRACT: The Federated States of Micronesia consists of four states of Yap, Chuuk, Pohnpei and Kosrae, which are located in the West Pacific Ocean. In order to investigate molluscan fauna of Kosrae Island, field survey was made twice from 21st to 30th of January, 2011 and from 6th to 17th of January, 2012 for four localities including 10 intertidal and 14 subtidal zones of Kosrae Island. The mollusk samples collected were identified based on their morphological characteristics, comprising a total of 120 species from 30 families through this survey. In this study, we provided species list and illustrations for 120 species identified, and combined these with the previous record, resulting in a total of 208 species from 47 families in Kosrae Island.
    The Korean Journal of Malacology. 01/2013; 29(4).
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    ABSTRACT: Despite recent advance in mass sequencing technologies such as pyrosequencing, assessment of culture-independent microbial eukaryote community structures using universal primers remains very difficult due to the tremendous richness and complexity of organisms in these communities. Use of a specific PCR marker targeting a particular group would provide enhanced sensitivity and more in-depth evaluation of microbial eukaryote communities compared to what can be achieved with universal primers. We discovered that many phylum-or groupspecific single-nucleotide polymorphisms (SNPs) exist in small subunit ribosomal RNA (SSU rRNA) genes from diverse eukaryote groups. By applying this discovery to a known simple allele-discriminating (SAP) PCR method, we developed a technique that enables the identification of organisms belonging to a specific higher taxonomic group (or phylum) among diverse types of eukaryotes. We performed an assay using two complementary methods, pyrosequencing and clone library screening. In doing this, specificities for the group (ciliates) targeted in this study in bulked environmental samples were 94.6% for the clone library and 99.2% for pyrosequencing, respectively. In particular, our novel technique showed high selectivity for rare species, a feature that may be more important than the ability to identify quantitatively predominant species in community structure analyses. Additionally, our data revealed that a target-specific library (or ciliate-specific one for the present study) can better explain the ecological features of a sampling locality than a universal library.
    Molecules and Cells 09/2012; 34:383–391. · 2.21 Impact Factor
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    ABSTRACT: An exponential growth of mitochondrial genome information has brought significant progress in understanding the organismal phylogeny and mitochondrial genome evolution for many metazoans including platyhelminth groups. In this study, we determined the complete mitochondrial genome sequence for Benedenia hoshinai, an ectoparasitic monogenean species, and compared it with its congener Benedenia seriolae. The complete mitochondrial genome is 13,554 bp in length and contains 12 protein-coding genes (lacking the atp8 gene), 2 rRNA genes, and 22 tRNA genes, all encoded in the same direction as found in all other platyhelminth species sequenced to date. The gene arrangement of B. hoshinai mtDNA is almost identical to B. seriolae, differing only by the translocation of trnT between cox1 and rrnL. It is unclear whether the shared position of trnT between B. hoshinai and Gyrodactylus represents evidence for their phylogenetic affinity; testing this hypothesis requires further mitogenomic evidence.
    Mitochondrial DNA 05/2012; 23(3):176-8. · 1.71 Impact Factor
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    ABSTRACT: Here, we report the first complete mitochondrial genome sequence of northern mauxia shrimp Acetes chinensis (Decapoda, Dendrobranchiata, Sergestoidae). The genome sequence was 15,740 bp in size, and the gene content, gene order and transcriptional polarity were almost identical to the pancrustacean ground pattern, with the one exception that an extra trnS(1)(AGC) was adjacent to the original trnS(1)(AGA). The two tandemly duplicated trnS(1) showed a high sequence similarity (82.3%), with almost identical secondary structure lacking a DHU arm. Comparison of codon usage suggests that both of the trnS(1) genes were functional.
    Mitochondrial DNA 02/2012; 23(1):28-30. · 1.71 Impact Factor
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    ABSTRACT: A major concern regarding the collection and storage of biodiversity information is the inefficiency of conventional taxonomic approaches in dealing with a large number of species. This inefficiency has increased the demand for automated, rapid, and reliable molecular identification systems and large-scale biological databases. DNA-based taxonomic approaches are now arguably a necessity in biodiversity studies. In particular, DNA barcoding using short DNA sequences provides an effective molecular tool for species identification. We constructed a large-scale database system that holds a collection of 5531 barcode sequences from 2429 Korean species. The Korea Barcode of Life database (KBOL, http://koreabarcode.org) is a web-based database system that is used for compiling a high volume of DNA barcode data and identifying unknown biological specimens. With the KBOL system, users can not only link DNA barcodes and biological information but can also undertake conservation activities, including environmental management, monitoring, and detecting significant organisms.
    Animal Cells and Systems. 02/2012; 16(1):11-19.
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    ABSTRACT: The Cymatium Roding, 1798 is a small- to large-sized marine gastropod genus. Three species has been reported thus far for Cymatium in the Korean waters. In general, Cymatium encausticum (Reeve, 1844) is known to occur in tropical seawaters including the Philippine Islands along with its congeners C. gutturnium, C. springsteeni, and C. exile. A single individual of the species was collected from Jejudo Island by SCUBA diving and morphological features were observed using a stereomicroscope. This is the first study to report the occurrence of Cymatium encausticum (Reeve, 1844) from the Korean waters, providing a detailed description of the species with the illustration for the shell morphology.
    Animal Systematics, Evolution and Diversity. 01/2012; 28(3).
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    ABSTRACT: In the present study, we determined the complete mitochondrial genome sequence of Oncicola luehei (14,281bp), the first archiacanthocephalan representative and the second complete sequence from the phylum Acanthocephala. The complete genome contains 36 genes including 12 protein coding genes, 22 transfer RNA (tRNA) genes and 2 ribosomal RNA genes (rrnL and rrnS) as reported for other syndermatan species. All genes are encoded on the same strand. The overall nucleotide composition of O. luehei mtDNA is 37.7% T, 29.6% G, 22.5% A, and 10.2% C. The overall A+T content (60.2%) is much lower, compared to other syndermatan species reported so far, due to the high frequency (18.3%) of valine encoded by GTN in its protein-coding genes. Results from phylogenetic analyses of amino acid sequences for 10 protein-coding genes from 41 representatives of major metazoan groups including O. luehei supported monophyly of the phylum Acanthocephala and of the clade Syndermata (Acanthocephala+Rotifera), and the paraphyly of the clade Eurotatoria (classes Bdelloidea+Monogononta from phylum Rotifera). Considering the position of the acanthocephalan species within Syndermata, it is inferred that obligatory parasitism characteristic of acanthocephalans was acquired after the common ancestor of acanthocephalans diverged from its sister group, Bdelloidea. Additional comparison of complete mtDNA sequences from unsampled acanthocephalan lineages, especially classes Polyacanthocephala and Eoacanthocephala, is required to test if mtDNA provides reliable information for the evolutionary relationships and pattern of life history diversification found in the syndermatan groups.
    Parasitology International 12/2011; 61(2):307-16. · 2.30 Impact Factor
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    ABSTRACT: The orders Ascaridida, Oxyurida, and Spirurida represent major components of zooparasitic nematode diversity, including many species of veterinary and medical importance. Phylum-wide nematode phylogenetic hypotheses have mainly been based on nuclear rDNA sequences, but more recently complete mitochondrial (mtDNA) gene sequences have provided another source of molecular information to evaluate relationships. Although there is much agreement between nuclear rDNA and mtDNA phylogenies, relationships among certain major clades are different. In this study we report that mtDNA sequences do not support the monophyly of Ascaridida, Oxyurida and Spirurida (clade III) in contrast to results for nuclear rDNA. Results from mtDNA genomes show promise as an additional independently evolving genome for developing phylogenetic hypotheses for nematodes, although substantially increased taxon sampling is needed for enhanced comparative value with nuclear rDNA. Ultimately, topological incongruence (and congruence) between nuclear rDNA and mtDNA phylogenetic hypotheses will need to be tested relative to additional independent loci that provide appropriate levels of resolution. For this comparative phylogenetic study, we determined the complete mitochondrial genome sequences of three nematode species, Cucullanus robustus (13,972 bp) representing Ascaridida, Wellcomia siamensis (14,128 bp) representing Oxyurida, and Heliconema longissimum (13,610 bp) representing Spirurida. These new sequences were used along with 33 published nematode mitochondrial genomes to investigate phylogenetic relationships among chromadorean orders. Phylogenetic analyses of both nucleotide and amino acid sequence datasets support the hypothesis that Ascaridida is nested within Rhabditida. The position of Oxyurida within Chromadorea varies among analyses; in most analyses this order is sister to the Ascaridida plus Rhabditida clade, with representative Spirurida forming a distinct clade, however, in one case Oxyurida is sister to Spirurida. Ascaridida, Oxyurida, and Spirurida (the sampled clade III taxa) do not form a monophyletic group based on complete mitochondrial DNA sequences. Tree topology tests revealed that constraining clade III taxa to be monophyletic, given the mtDNA datasets analyzed, was a significantly worse result. The phylogenetic hypotheses from comparative analysis of the complete mitochondrial genome data (analysis of nucleotide and amino acid datasets, and nucleotide data excluding 3rd positions) indicates that nematodes representing Ascaridida, Oxyurida and Spirurida do not share an exclusive most recent common ancestor, in contrast to published results based on nuclear ribosomal DNA. Overall, mtDNA genome data provides reliable support for nematode relationships that often corroborates findings based on nuclear rDNA. It is anticipated that additional taxonomic sampling will provide a wealth of information on mitochondrial genome evolution and sequence data for developing phylogenetic hypotheses for the phylum Nematoda.
    BMC Genomics 08/2011; 12:392. · 4.40 Impact Factor
  • Yung Chul Park, Won Kim, Joong-Ki Park
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    ABSTRACT: The genome length of the Ascaris lumbricoides, human parasitic roundworm, is 14,281 bp with a nucleotide composition of 22.1% A, 49.8% T, 7.8% C, and 20.3% G. The genome consists of 12 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region.
    Mitochondrial DNA 08/2011; 22(4):91-3. · 1.71 Impact Factor
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    ABSTRACT: We determined a full-length sequence of mitochondrial (mt) genome from Upogebia major. This is the first complete mt genome report for infraorder Thalassinidea in Decapoda, Crustacea. Our result showed that U. major generally followed a typical pancrustacean gene order but some tRNA genes showed a very unique gene arrangement such as duplication or translocation. Since none of the complete mt genome sequences in the infraorder Thalassinidea are available yet, this report will provide additional information in relation to mt genome diversity and evolution of the decapods.
    Mitochondrial DNA 08/2011; 22(4):94-6. · 1.71 Impact Factor

Publication Stats

280 Citations
67.03 Total Impact Points

Institutions

  • 2011–2013
    • Korea Polar Research Institute
      Sŏul, Seoul, South Korea
    • Kangwon National University
      • Department of Forest Environment Protection
      Kang-neung, Gangwon, South Korea
  • 2009–2013
    • Inha University
      • Department of Biological Sciences
      Seoul, Seoul, South Korea
  • 2004–2013
    • Chungbuk National University
      • • College of Medicine
      • • Department of Parasitology and Medical Research Institute
      Chinsen, North Chungcheong, South Korea
  • 2002
    • Seoul National University
      • Department of Biological Sciences
      Seoul, Seoul, South Korea