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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 | 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.

Park B.M.,Chonnam National University | Patnaik B.B.,Chonnam National University | Oh S.,Chonnam National University | Kim D.H.,Chonnam National University | And 6 more authors.
Entomological Research | Year: 2013

The tumor suppressor, QM has been cloned and characterized from eukaryotic organisms including humans, vertebrates, invertebrates, plants and yeast. However, no study on Pieris rapaeQM (PrQM) has been reported to date. In this study, cDNA encoding a putative QM protein (PrQM) was obtained from expressed sequence tags (ESTs) of the Pieris rapaecDNA library. Phylogenetic analysis of PrQM showed high similarity of amino acid sequence with other putative homologues identified from Heliothis virescens (95%), Bombyx mori (92%), Plutella xylostella (92%), Drosophila melanogaster (89%) and Polyrhachis vicina (85%), indicating that QM is highly conserved among insects. Semi-quantitative PCR datasets revealed that PrQM transcripts are highly expressed in head, silk gland, integument and fat body, with pronounced expression observed during the egg stage. The coding region of the PrQM gene was cloned into the pET28 (+) expression vector and the recombinant protein purified by His-tag affinity chromatography was used for antibody production. Western blotting with the anti-PrQM antibody detected a single band corresponding to the expected molecular weight of both endogenous (26kDa) and recombinant (29kDa) PrQM. Furthermore, immunohistochemical and confocal microscopic analysis with the anti-PrQM antibody showed that the QM gene is highly expressed in the cytoplasm of fat body, gut and Malpighian tubules in virus-uninfected control larvae, but down-regulated at 4 days post Pieris rapae granulovirus (PiraGV) infection. These data show that PrQM is negatively regulated upon virus infection and suggests a putative immunomodulatory function. © 2013 The Entomological Society of Korea and Wiley Publishing Asia Pty Ltd.

Wang A.R.,Chonnam National University | Jeong H.C.,Hampyeong County Insect Institute | Han Y.S.,Chonnam National University | Kim I.,Chonnam National University
Mitochondrial DNA | Year: 2014

The mountainous duskywing, Erynnis montanus, belongs to a lepidopteran family Hesperiidae. The 15,530-bp long complete mitochondrial genome (mitogenome) of the species has the typical gene content of animals (13 protein-coding genes, two rRNA genes, 22 tRNA genes and one major non-coding A+T-rich region). As typical in lepidopteran mitogenome E. montanus mitogenome also contained a high A/T content in the whole genome (81.7%) and the CGA (arginine) as the start codon for the COI gene. Unlike other lepidopteran species, including two sequenced skippers, the E. montanus mitogenome has a unique arrangement tRNASer-tRNAAsn, instead of the tRNAAsn-tRNASer found unanimously in other lepidopteran species, providing a new gene arrangement in Lepidoptera. Such rearrangement probably was likely caused by duplication of gene block tRNASer- tRNAAsn and subsequent random loss of tRNAAsn in the first copy and tRNASer in the second copy, resulting in the arrangement tRNASer-tRNAAsn. © 2014 Informa UK Ltd.

Jo Y.H.,Chonnam National University | Patnaik B.B.,Chonnam National University | Kang S.W.,Soonchunhyang University | Chae S.-H.,GnC BIO Co. | And 11 more authors.
PLoS ONE | Year: 2013

Background: Most traditional genome sequencing projects involving viruses include the culture and purification of the virus particles. However, purification of virions may yield insufficient material for traditional sequencing. The electrophoretic method described here provides a strategy whereby the genomic DNA of the Korean isolate of Pieris rapae granulovirus (PiraGV-K) could be recovered in sufficient amounts for sequencing by purifying it directly from total host DNA by pulse-field gel electrophoresis (PFGE). Methodology/Principal Findings: The total genomic DNA of infected P. rapae was embedded in agarose plugs, treated with restriction nuclease and methylase, and then PFGE was used to separate PiraGV-K DNA from the DNA of P. rapae, followed by mapping of fosmid clones of the purified viral DNA. The double-stranded circular genome of PiraGV-K was found to encode 120 open reading frames (ORFs), which covered 92% of the sequence. BLAST and ORF arrangement showed the presence of 78 homologs to other genes in the database. The mean overall amino acid identity of PiraGV-K ORFs was highest with the Chinese isolate of PiraGV (∼99%), followed up with Choristoneura occidentalis ORFs at 58%. PiraGV-K ORFs were grouped, according to function, into 10 genes involved in transcription, 11 involved in replication, 25 structural protein genes, and 15 auxiliary genes. Genes for Chitinase (ORF 10) and cathepsin (ORF 11), involved in the liquefaction of the host, were found in the genome. Conclusions/ Significance: The recovery of PiraGV-K DNA genome by pulse-field electrophoretic separation from host genomic DNA had several advantages, compared with its isolation from particles harvested as virions or inclusions from the P. rapae host. We have sequenced and analyzed the 108,658 bp PiraGV-K genome purified by the electrophoretic method. The method appears to be generally applicable to the analysis of genomes of large viruses. © 2013 Jo et al.

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