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Patnaik B.B.,Soonchunhyang University | Patnaik B.B.,Trident Academy of Creative Technology TACT | Hwang H.-J.,Soonchunhyang University | Kang S.W.,Soonchunhyang University | And 12 more authors.
International Journal of Molecular Sciences | Year: 2015

The Lycaenidae butterflies, Protantigius superans and Spindasis takanosis, are endangered insects in Korea known for their symbiotic association with ants. However, necessary genomic and transcriptomics data are lacking in these species, limiting conservation efforts. In this study, the P. superans and S. takanosis transcriptomes were deciphered using Illumina HiSeq 2500 sequencing. The P. superans and S. takanosis transcriptome data included a total of 254,340,693 and 245,110,582 clean reads assembled into 159,074 and 170,449 contigs and 107,950 and 121,140 unigenes, respectively. BLASTX hits (E-value of 1.0 × 10-5) against the known protein databases annotated a total of 46,754 and 51,908 transcripts for P. superans and S. takanosis. Approximately 41.25% and 38.68% of the unigenes for P. superans and S. takanosis found homologous sequences in Protostome DB (PANM-DB). BLAST2GO analysis confirmed 18,611 unigenes representing Gene Ontology (GO) terms and a total of 5259 unigenes assigned to 116 pathways for P. superans. For S. takanosis, a total of 6697 unigenes were assigned to 119 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Additionally, 382,164 and 390,516 Simple Sequence Repeats (SSRs) were compiled from the unigenes of P. superans and S. takanosis, respectively. This is the first report to record new genes and their utilization for conservation of lycaenid species population and as a reference information for closely related species. © 2015 by the authors; licensee MDPI, Basel, Switzerland.


Patnaik B.B.,Soonchunhyang University | Patnaik B.B.,Trident Academy of Creative Technology TACT | Wang T.H.,Soonchunhyang University | Kang S.W.,Soonchunhyang University | And 11 more authors.
PLoS ONE | Year: 2016

Background: The freshwater mussel Cristaria plicata (Bivalvia: Eulamellibranchia: Unionidae), is an economically important species in molluscan aquaculture due to its use in pearl farming. The species have been listed as endangered in South Korea due to the loss of natural habitats caused by anthropogenic activities. The decreasing population and a lack of genomic information on the species is concerning for environmentalists and conservationists. In this study, we conducted a de novo transcriptome sequencing and annotation analysis of C. plicata using Illumina HiSeq 2500 next-generation sequencing (NGS) technology, the Trinity assembler, and bioinformatics databases to prepare a sustainable resource for the identification of candidate genes involved in immunity, defense, and reproduction. Results: The C. plicata transcriptome analysis included a total of 286,152,584 raw reads and 281,322,837 clean reads. The de novo assembly identified a total of 453,931 contigs and 374,794 non-redundant unigenes with average lengths of 731.2 and 737.1 bp, respectively. Furthermore, 100% coverage of C. plicata mitochondrial genes within two unigenes supported the quality of the assembler. In total, 84,274 unigenes showed homology to entries in at least one database, and 23,246 unigenes were allocated to one or more Gene Ontology (GO) terms. The most prominent GO biological process, cellular component, and molecular function categories (level 2) were cellular process, membrane, and binding, respectively. A total of 4,776 unigenes were mapped to 123 biological pathways in the KEGG database. Based on the GO terms and KEGG annotation, the unigenes were suggested to be involved in immunity, stress responses, sex-determination, and reproduction. A total of 17,251 cDNA simple sequence repeats (cSSRs) were identified from 61,141 unigenes (size of >1 kb) with the most abundant being dinucleotide repeats. Conclusions: This dataset represents the first transcriptome analysis of the endangered mollusc, C. plicata. The transcriptome provides a comprehensive sequence resource for the conservation of genetic information in this species and enrichment of the genetic database. The development of molecular markers will assist in the genetic improvement of C. plicata. © 2016 Patnaik et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


Jeong J.E.,Dong - A University | Kang S.W.,Soonchunhyang University | Hwang H.-J.,Soonchunhyang University | Park S.Y.,Soonchunhyang University | And 13 more authors.
Genes and Genomics | Year: 2015

Pisidium (Neopisidium) coreanum is a freshwater clam endemic to Korea. It has been classified as a vulnerable bivalve by the Korean Red List of threatened species and there exist no regional conservation measures. In the present study, we made an attempt to study the expressed sequence tags (ESTs) from the clam species for elucidating genomic information through the annotation of essential genes. A high-quality cDNA library was constructed from the whole body tissue of Pisidium coreanum yielding a collection of 5760 clones. The sequencing of the resultant clones identified 5656 ESTs assembled into 1312 non-redundant sequences, comprising of 791 contigs and 521 singletons. We identified 3265 and 3314 EST sequences showing significant matches (E value <1e−5) to known sequences in the mollusks sequence database (Malacological Society of Korea) and the NCBI non-redundant database, respectively. A total of 1674 putative sequences showed significant matches (E value of 1e−10) with the National Centre for Biotechnology Information-Eukaryotic Clusters of Orthologous Groups (NCBI KOG) database. These sequences were successfully assigned to classified biological processes including translation, ribosomal structure and biogenesis (18.61 %), post-translational modification, protein turnover and chaperones (13.29 %), energy production and conversion (13.86 %), cytoskeleton (12.78 %), and signal transduction mechanisms (7.15 %). Furthermore, we identified 16 transcripts showing high homology with bone morphogenetic protein 2-B that could pave an advancement towards bone therapeutics development. © 2015, The Genetics Society of Korea and Springer-Science and Media.


Patnaik B.B.,Soonchunhyang University | Patnaik B.B.,Trident Academy of Creative Technology TACT | Park S.Y.,Soonchunhyang University | Kang S.W.,Soonchunhyang University | And 12 more authors.
International Journal of Genomics | Year: 2016

Vespa mandarinia found in the forests of East Asia, including Korea, occupies the highest rank in the arthropod food web within its geographical range. It serves as a source of nutrition in the form of Vespa amino acid mixture and is listed as a threatened species, although no conservation measures have been implemented. Here, we performed de novo assembly of the V. mandarinia transcriptome by Illumina HiSeq 4000 sequencing. Over 60 million raw reads and 59,184,811 clean reads were obtained. After assembly, a total of 66,837 unigenes were clustered, 40,887, 44,455, and 22,390 of which showed homologous matches against the PANM, Unigene, and KOG databases, respectively. A total of 15,675 unigenes were assigned to Gene Ontology terms, and 5,132 unigenes were mapped to 115 KEGG pathways. The zinc finger domain (C2H2-like), serine/threonine/dual specificity protein kinase domain, and RNA recognition motif domain were among the top InterProScan domains predicted for V. mandarinia sequences. Among the unigenes, we identified 534,922 cDNA simple sequence repeats as potential markers. This is the first transcriptomic analysis of the wasp V. mandarinia using Illumina HiSeq 4000. The obtained datasets should promote the search for new genes to understand the physiological attributes of this wasp. © 2016 Bharat Bhusan Patnaik et al.


Lee Y.S.,Inje University | Lee S.-G.,South Korean National Institute of Animal Science | Kang S.W.,Inje University | Jeong J.E.,Inje University | And 6 more authors.
Journal of Shellfish Research | Year: 2011

Physa acuta (left-handed shell) have strong natural growth activity not only in lentic waters but also in eutrophic environments. Therefore, it has been considered one of the candidate species that could evaluate the degree of water pollution by physiological and biochemical methods. In this study, we constructed a P. acuta cDNA library using the 5′ oligo capping method, and determined the sequences of 2,282 clones by 5′ end-single path sequencing. After trimming, clustering, and assembling these sequences, we finally obtained 575 distinctly available transcripts that were 718 bp in average length. These transcripts were annotated using the BLASTX search and were classified by function using KOG analysis. After comparison with biomarker genes already known in several organisms, we identified 27 potential biomarker candidates that were categorized into two groups strongly related to stress and defense genes by their functions. To the best of our knowledge, this is the first report of massive profiling of cDNA sequences and the characterizing of potential biomarker genes in P. acuta. Our study offers valuable information to scientists for developing new environmental biomonitoring markers, and for scientists studying the physiology, growth and development, immunity, genetic identification, and evolutional diversity in P. acuta.

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