동양달팽이 (Nesiohelix samarangae) 의 expressed sequence tags (ESTs) 로부터 분리한 2종류의 Serpin 유전자 분석

박소영,정지은,황희주,왕태훈,박은비,김용민,이준상,한연수,양승하,이용석,Park, So Young,Jeong, Ji Eun,Hwang, Hee Ju,Wang, Tae Hun,Park, Eun Bi,Kim, Yong Min,Lee, Jun-Sang,Han, Yeon Soo,Yang, Seung-Ha,Lee, Yong Seok 한국패류학회 2014 The Korean Journal of Malacology Vol.30 No.2

동양달팽이의 EST 에서 serpin 유전자는 2가지 type이 추정되었다. Ns-serpin type 1 (partial) 서열의 코딩 영역은 총 819 bp 이었으며, 272개의 아미노산으로 이루어져 있었으며, Ns-serpin type 2 (partial) 의 코딩영역은 총 555 bp, 185개의 아미노산으로 이루어져 있었다. Laminarin 처리 전에는 Ns-serpin type 1이 2개 발현되었으며 처리 후에는 Ns-serpin type 2가 1개 발현되고 있었다. BLAST 결과를 바탕으로 유사도가 높은 17개의 참고 서열과 동양달팽이의 Ns-serpin type 1, 2의 아미노산 서열을 MEGA6 프로그램의 clustalW 엔진을 이용하여 multiple sequence alignment 를 수행한 결과, 척색동물의 포유강 9종, 조류강 1종, 양서강 1종과 척색동물인 해초강, 절지동물의 거미강 1종과 곤충강 1종이 같은 군으로 묶였으며, 연체동물문의 경우 동양달팽이의 두 가지 type 을 포함한 복족강 4종이 같은 군으로 묶이는 것을 확인하였다. Psipred 프로그램을 활용하여 예측한 2D 구조도 multiple align 및 phylodendrogram 결과와 연관이 있음을 확인할 수 있었다. EST를 통해 밝힌 동양달팽이의 두 가지 type의 Ns-serpin 서열은 Aplysia californica 등의 근연종들의 서열과 유사하였다. 본 연구에서는 무척추동물에서의 선천성 면역과 연관이 있는 것으로 잘 알려진 두 종류의 serpin 유전자 서열을 동양달팽이 EST 결과에서 발굴 하였으며, 동양달팽이에서도 여러 가지 type의 serpin 이 존재 할 수 있음을 입증하였다. Serpins are a group of proteins involved in the regulation of serine and other type of proteases, and have been identified in many kinds of organisms from invertebrates to vertebrates. Serpins are known to regulate the proteolytic cascades of the innate immune pathways in addition to their roles in blood coagulation, angiogenesis, fibrinolysis, inflammation and tumor suppression. In this study, we have isolated two partial serpin gene fragments from expressed sequence tags (ESTs) of Nesiohelix samarangae. Dotplot analysis indicates that they are of two different types, Ns-serpin type 1 and Ns-serpin type 2. Ns-serpin type 1 has 819 bp coding region (272 amino acids), whereas Ns-serpin type 2 has 555 bp coding region (185 amino acids). Molecular phylogenetic analysis shows that the identified serpins have high similarities to their counterparts in the California see slug, Aplysia californica. Yet, the precise biological and immunological roles of these Ns-serpins remain to be further investigated using RNA interference and other molecular techniques.

연체동물 전용 BLAST 서버 업데이트 (Version II)

강세원,황희주,박소영,왕태훈,박은비,이태희,황의욱,이준상,박홍석,한연수,임채은,김순옥,이용석 한국패류학회 2014 The Korean Journal of Malacology Vol.30 No.4

Since we reported a BLAST server for the mollusk in 2004, no work has reported the usability or modification of the server. To improve its usability, the BLAST server for the mollusk has been updated as version II (http://www.malacol.or.kr/blast) in the present study. The database was constructed by using the Intel server Platform ZSS130 dual Xeon 3.20 GHz CPU and Linux CentOS system and with NCBI WebBLAST package. We downloaded the mollusk nucleotide, amino acid, EST, GSS and mitochondrial genome sequences which can be opened through NCBI web BLAST and used them to build up the database. The updated database consists of 520,977 nucleotide sequences, 229,857 amino acid sequences, 586,498 EST sequences, 23,112 GSS and 565 mitochondrial genome sequences. Total database size is 1.2 GB. Furthermore, we have added repeat sequences, Escherichia coli sequences and vector sequences to facilitate data validation. The newly updated BLAST server for the mollusk will be useful for many malacological researchers as it will save time to identify and study various molluscan genes. 본 연구를 통하여 연체동물 전용 BLAST 서버 (Version II) 가 웹주소 http://www.malacol.or.kr/blast 에 구축되었다. 연체동물을 대상으로 하는 연구에 있어 필요한 정보를 매우 빠르게 얻을 수 있었다. 본 시스템을 사용하여 앞으로도 많은 연구가 진행되어지길 바라며, 아울러 많은 연체동물 연구자들에게 많은 도움이 되리라고 사료된다.

RNA sequencing, de novo assembly, and functional annotation of an endangered Nymphalid butterfly, Fabriciana nerippe Felder, 1862

황희주,Bharat Bhusan Patnaik,강세원,박소영,왕태훈,박은비,정종민,송대권,Hongray Howrelia PATNAIK,김창무,김순옥,이재봉,정헌천,박홍석,한연수,이용석 한국곤충학회 2016 Entomological Research Vol.46 No.2

Grassland butterflies are considered representative indicators of biodiversity and ecosystem health. Their dramatic decline caused by habitat destruction, intensifying agriculture and global warming has prompted concern for conservation. While ecological indices of butterflies have been documented, there is a lack of genomic resources relative to the biological importance of this group. Here, we report, first whole‐transcriptomic resource for Fabriciana nerippe, a brush‐footed butterfly member that is endangered in Korea. Approximately, 241.3 million clean reads were obtained from paired‐end Illumina sequencing of adult whole‐body RNA. The de novo assembly resulted in 114 405 unigenes with length ranging from 133 to 33 218 bp. We found 41 868 assembled unigenes homologous to sequences in locally curated PANM‐DB (Protostome DB). We assigned gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology terms to 18 085 and 5779 unigenes, respectively. InterProScan predicted 6691 protein domains for the assembled unigene sequences, with the reverse transcriptase and zinc finger domains found to be the most predominant. A total of 315 282 simple sequence repeats (SSRs) were identified from the assembled unigenes, when considering dinucleotide to octanucleotide repeats with a minimum of three repeat units. AT/AT, AAT/ATT, and AAAT/ATTT represented the most prominent SSR repeat types in the transcriptome. The unigene annotation profile and microsatellites generated in the study can serve as a reference resource for closely related species and gene functional analysis studies. Our data can be utilized to study ecological drift and loss of the species, consequently leading to better protection of the population.

Characterization of Physa acuta expressed sequence tags and transcript mining following cadmium exposure

정지은,패트나익,강세원,황희주,박소영,왕태훈,박은비,이재봉,남명모,조용훈,한연수,이준상,박홍석,이용석 한국유전학회 2015 Genes & Genomics Vol.37 No.12

Freshwater molluscs have found strategic applications in public and veterinary health. Additionally, they have been used as bioindicator organisms towards environmental biomonitoring of polluted waters. The freshwater pulmonate, Physa acuta has been extensively studied as a potential biomarker in aquatic habitats with heavy metal, chemical, and microbial stressors. Lack of genomic resources is the bottleneck towards the study of candidate genes responsible for the unique adaptation of the mollusc to contaminated aquatic habitats. We have reported an EST survey of functionally relevant stress and defense related genes from P. acuta in our earlier study. In continuation of the same, we generated 1108 high-quality ESTs from a normalized cDNA library, pooled from the RNA isolated from the whole body tissue of CdCl2 exposed specimens of P. acuta. After clustering and assembly, we finally obtained 730 unique sequences representing 114 contigs and 616 singletons. Annotation of EST sequences revealed that 65.2, 62.8, and 35.9 % show significant homology to NCBI non-redundant database, Molluscs amino acid database, and NCBI KOG database, respectively. The functional characterization of the ESTs in Cd treated P. acuta group showed a greater proportion of signal transduction, cytoskeleton, and extracellular structure relevant genes compared with the control group. A large proportion of transcripts of cadmium treated P. acuta fell under the poorly characterized group of genes. These EST resources provide valuable information on Cd-specific transcript expression of P. acuta and could be utilized by scientists for developing new biomonitoring markers.

Expressed sequence tag analysis and annotation of genetic information from the freshwater clam, Pisidium (Neopisidium) coreanum endemic to Korea

정지은,강세원,황희주,박소영,패트나익,김창무,김순옥,남명모,이재봉,왕태훈,박은비,이순신,한연수,이준상,박홍석,이용석 한국유전학회 2015 Genes & Genomics Vol.37 No.12

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.