• Title, Summary, Keyword: EST (Expressed Sequence Tag)

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Spliced leader sequences detected in EST data of the dinoflagellates Cochlodinium polykrikoides and Prorocentrum minimum

  • Guo, Ruoyu;Ki, Jang-Seu
    • ALGAE
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    • v.26 no.3
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    • pp.229-235
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    • 2011
  • Spliced leader (SL) trans-splicing is a mRNA processing mechanism in dinoflagellate nuclear genes. Although studies have identified a short, conserved dinoflagellate SL (dinoSL) sequence (22-nt) in their nuclear-encoded transcripts, whether the majority of nuclear-coded transcripts in dinoflagellates have the dinoSL sequence remains doubtful. In this study, we investigated dinoSL-containing gene transcripts using 454 pyrosequencing data (Cochlodinium polykrikoides, 93 K sequence reads, 31 Mb; Prorocentrum minimum, 773 K sequence reads, 291 Mb). After making comparisons and performing local BLAST searches, we identified dinoSL for one C. polykrikoides gene transcript and eight P. minimum gene transcripts. This showed transcripts containing the dinoSL sequence were markedly fewer in number than the total expressed sequence tag (EST) transcripts. In addition, we found no direct evidence to prove that most dinoflagellate nuclear-coded transcripts have this dinoSL sequence.

Bioinformatics in Fish: its Present Status and Perspectives with Particular Emphasis on Expressed Sequence Tags

  • Nam, Yoon-Kwon;Kim, Dong-Soo
    • Journal of Aquaculture
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    • v.14 no.1
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    • pp.9-16
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    • 2001
  • Characterization of a single pass of cDNA sequence, an expressed sequence tag (EST) has been a fast growing activity in fish genomics. Despite its relatively short history, fish EST databases (dbESTs) have already begun to play a significant role in bridging the gaps in our knowledge on the gene expression in fish genome. This review provides a brief description of the technology for establishing fish dbESTs, its current status, and implication of the ESTs to aquaculture and fisheries science with particular emphasis on the discovery of novel genes for transgenic application, the use of polymorphic EST markers in genetic linkage mapping and the evaluation of signal-responsive gene expression.

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Immune Gene Discovery by Expressed Sequence Tags Generated from Olive Flounder (Paralichthys olivaceus) Kidney (넙치 (Paralichthys olivaceus) 신장에서 생성된 ESTs (Expressed Sequence Tags)로부터 면역관련 유전자의 탐색)

  • Lee, Jeong-Ho;Kim, Young-Ok;Kim, Jong-Hyun;Noh, Jae Koo;Kim, Hyun Chul;Kim, Kyung-Kil;Kim, Kyu-Won
    • Korean Journal of Ichthyology
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    • v.18 no.4
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    • pp.283-292
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    • 2006
  • Expressed sequence tag (EST) analysis was conducted using a complementary DNA (cDNA) library made from the kidney mRNA of olive flounder (Paralichthys olivaceus). In the survey of 390 ESTs chosen from the kidney cDNA library, 250 ESTs showed significant homology to previously described genes while 140 ESTs were unidentified or novel. Comparative analysis of the 250 identified ESTs showed that 14 (5.6%) clones were representing 11 unique genes identified as homologous to the previously reported olive flounder ESTs, 198 (79.2%) clones representing 160 unique genes were identified as orthologs of known genes from other organisms, and orthologs were established for 38 (15.2%) clones representing 37 genes of known sequences with unknown functions. We also identified several kinds of immune associated proteins, indicating EST as a powerful method for identifying immunerelated genes of fish as well as identifying novel genes. Further studies using cDNA microarrays are needed to identify the differentially expressed transcripts after disease infection.

Expressed Sequence Tags of Expression Profiles of Olive Flounder (Paralichthys olivaceus) Testis (ESTs (Expressed Sequence Tags)를 통한 넙치(Paralichthys olivaceus) 정소의 유전자 발현 패턴 분석)

  • Lee, Jeong-Ho;Kim, Jong-Hyun;Noh, Jae Koo;Kim, Hyun Chul;Kim, Young-Ok;Kim, Woo-Jin;Kim, Kyu-Won;Kim, Kyung-Kil
    • Korean Journal of Ichthyology
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    • v.19 no.4
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    • pp.257-265
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    • 2007
  • We constructed a cDNA library of testis from olive flounder (Paralichthys olivaceus) and a total of 248 expressed sequence tag (EST) clones were generated. In order to understand the molecular compositions of the olive flounder testis organs, the expression profiles of the identified clones in the cDNA library were analyzed. Gene annotation procedures and homology searches of the sequenced ESTs were locally done by BLASTX for amino acid similarity comparisons. Of the 248 EST clones, 156 ESTs showed significant homology to previously described genes while 92 ESTs were unidentified or novel. Comparative analysis of the 156 identified ESTs showed that 6 (3.8%) clones were representing 5 unique genes identified as homologous to the previously reported olive flounder ESTs, 100 (64.1%) clones representing 94 unique genes were identified as orthologs of known genes from other organisms, and orthologs were established for 50 (32.1%) clones representing 44 genes of known sequences with unknown functions. Furthermore, the testis library showed a more even distribution of cDNA clones with relatively fewer abundant clones that tend to contribute redundant clones in EST projects; thus, the testis library can supply more unique and novel cDNA sequences in olive flounder EST project.

Proteome Data Analysis of Hairy Root of Panax ginseng : Use of Expressed Sequence Tag Data of Ginseng for the Protein Identification (인삼 모상근 프로테옴 데이터 분석 : 인삼 EST database와의 통합 분석에 의한 단백질 동정)

  • Kwon, Kyung-Hoon;Kim, Seung-Il;Kim, Kyung-Wook;Kim, Eun-A;Cho, Kun;Kim, Jin-Young;Kim, Young-Hwan;Yang, Deok-Chun;Hur, Cheol-Goo;Yoo, Jong-Shin;Park, Young-Mok
    • Journal of Plant Biotechnology
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    • v.29 no.3
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    • pp.161-170
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    • 2002
  • For the hairy root of Panax ginseng, we have got mass spectrums from MALDI/TOF/MS analysis and Tandem mass spectrums from ESI/Q-TOF/MS analysis. While mass spectrum provides the molecular weights of peptide fragments digested by protease such as trypsin, tandem mass spectrum produces amino acid sequence of digested peptides. Each amino acid sequences can be a query sequence in BLAST search to identify proteins. For the specimens of animals or plants of which genome sequences were known, we can easily identify expressed proteins from mass spectrums with high accuracy. However, for the other specimens such as ginseng, it is difficult to identify proteins with accuracy since all the protein sequences are not available yet. Here we compared the mass spectrums and the peptide amino acid sequences with ginseng expressed sequence tag (EST) DB. The matched EST sequence was used as a query in BLAST search for protein identification. They could offer the correct protein information by the sequence alignment with EST sequences. 90% of peptide sequences of ESI/Q-TOF/MS are matched with EST sequences. Comparing 68% matches of the same sequences with the nr database of NCBI, we got more matches by 22% from ginseng EST sequence search. In case of peptide mass fingerprinting from MALDI/TOF/MS, only about 19% (9 proteins of 47 spots) among peptide matches from nr DB were correlated with ginseng EST DB. From these results, we suggest that amino acid sequencing using tandem mass spectrum analysis may be necessary for protein identification in ginseng proteome analysis.

Expressed Sequence Tag Analysis of the Erythrocytic Stage of Plasmodium berghei

  • Seok, Ji-Woong;Lee, Yong-Seok;Moon, Eun-Kyung;Lee, Jung-Yub;Jha, Bijay Kumar;Kong, Hyun-Hee;Chung, Dong-Il;Hong, Yeon-Chul
    • The Korean Journal of Parasitology
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    • v.49 no.3
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    • pp.221-228
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    • 2011
  • Rodent malaria parasites, such as Plasmodium berghei, are practical and useful model organisms for human malaria research because of their analogies to the human malaria in terms of structure, physiology, and life cycle. Exploiting the available genetic sequence information, we constructed a cDNA library from the erythrocytic stages of P. berghei and analyzed the expressed sequence tag (EST). A total of 10,040 ESTs were generated and assembled into 2,462 clusters. These EST clusters were compared against public protein databases and 48 putative new transcripts, most of which were hypothetical proteins with unknown function, were identified. Genes encoding ribosomal or membrane proteins and purine nucleotide phosphorylases were highly abundant clusters in P. berghei. Protein domain analyses and the Gene Ontology functional categorization revealed translation/protein folding, metabolism, protein degradation, and multiple family of variant antigens to be mainly prevalent. The presently-collected ESTs and its bioinformatic analysis will be useful resources to identify for drug target and vaccine candidates and validate gene predictions of P. berghei.

Confirming Single Nucleotide Polymorphisms from Expressed Sequence Tag Datasets Derived from Three Cattle cDNA Libraries

  • Lee, Seung-Hwan;Park, Eung-Woo;Cho, Yong-Min;Lee, Ji-Woong;Kim, Hyoung-Yong;Lee, Jun-Heon;Oh, Sung-Jong;Cheong, Il-Cheong;Yoon, Du-Hak
    • BMB Reports
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    • v.39 no.2
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    • pp.183-188
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    • 2006
  • Using the Phred/Phrap/Polyphred/Consed pipeline established in the National Livestock Research Institute of Korea, we predicted candidate coding single nucleotide polymorphisms (cSNPs) from 7,600 expressed sequence tags (ESTs) derived from three cDNA libraries (liver, M. longissimus dorsi, and intermuscular fat) of Hanwoo (Korean native cattle) steers. From the 7,600 ESTs, 829 contigs comprising more than two EST reads were assembled using the Phrap assembler. Based on the contig analysis, 201 candidate cSNPs were identified in 129 contigs, in which transitions (69%) outnumbered transversions (31%). To verify whether the predicted cSNPs are real, 17 SNPs involved in lipid and energy metabolism were selected from the ESTs. Twelve of these were confirmed to be real while five were identified as artifacts, possibly due to expressed sequence tag sequence error. Further analysis of the 12 verified cSNPs was performed using the program BLASTX. Five were identified as nonsynonymous cSNPs, five were synonymous cSNPs, and two SNPs were located in 3'-UTRs. Our data indicated that a relatively high SNP prediction rate (71%) from a large EST database could produce abundant cSNPs rapidly, which can be used as valuable genetic markers in cattle.

Expressed sequence tags analysis of immune-relevant genes in rock bream Oplegnathus fasciatus gill stimulated with LPS

  • Lee, Jeong-Ho;Kim, Ju-Won;Baeck, Gun-Wook;Park, Chan-Il
    • Journal of fish pathology
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    • v.23 no.3
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    • pp.429-440
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    • 2010
  • We constructed a rock bream (Oplegnathus fasciatus) gill cDNA library and a total of 1450 expressed sequence tag (EST) clones were generated. Gene annotation procedures and homology searches of the sequenced ESTs were locally done by BLASTX for amino acid similarity comparisons. Of the 1450 EST clones, 1022 EST clones showed significant homology to previously described genes while 428 ESTs were unidentified, and 259 clones were hypothetical, or unnamed proteins. Encoding 313 different sequences were identified as putative bio-defense genes or genes associated with immune response.

Development and Validation of Single Nucleotide Polymorphism (SNP) Markers from an Expressed Sequence Tag (EST) Database in Olive Flounder (Paralichthys olivaceus)

  • Kim, Jung Eun;Lee, Young Mee;Lee, Jeong-Ho;Noh, Jae Koo;Kim, Hyun Chul;Park, Choul-Ji;Park, Jong-Won;Kim, Kyung-Kil
    • Development and Reproduction
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    • v.18 no.4
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    • pp.275-286
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    • 2014
  • To successful molecular breeding, identification and functional characterization of breeding related genes and development of molecular breeding techniques using DNA markers are essential. Although the development of a useful marker is difficult in the aspect of time, cost and effort, many markers are being developed to be used in molecular breeding and developed markers have been used in many fields. Single nucleotide polymorphisms (SNPs) markers were widely used for genomic research and breeding, but has hardly been validated for screening functional genes in olive flounder. We identified single nucleotide polymorphisms (SNPs) from expressed sequence tag (EST) database in olive flounder; out of a total 4,327 ESTs, 693 contigs and 514 SNPs were detected in total EST, and these substitutions include 297 transitions and 217 transversions. As a result, 144 SNP markers were developed on the basis of 514 SNP to selection of useful gene region, and then applied to each of eight wild and culture olive flounder (total 16 samples). In our experimental result, only 32 markers had detected polymorphism in sample, also identified 21 transitions and 11 transversions, whereas indel was not detected in polymorphic SNPs. Heterozygosity of wild and cultured olive flounder using the 32 SNP markers is 0.34 and 0.29, respectively. In conclusion, we identified SNP and polymorphism in olive flounder using newly designed marker, it supports that developed markers are suitable for SNP detection and diversity analysis in olive flounder. The outcome of this study can be basic data for researches for immunity gene and characteristic with SNP.

Survey of Expressed Sequence Tags from Tissue-Specific cDNA Libraries in Hemibarbus mylodon, an Endangered Fish Species (멸종위기 어류 어름치 Hemibarbus mylodon (Cypriniformes)로부터 조직별 EST library 제작 및 발현 유전자 탐색)

  • Bang, In-Chul;Lim, Yoon-Hee;Cho, Young-Sun;Lee, Sang-Yoon;Nam, Yoon-Kwon
    • Journal of Aquaculture
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    • v.20 no.4
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    • pp.248-254
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    • 2007
  • Representative cDNA libraries were constructed from various tissue sources of Hemibarbus mylodon, an endangered freshwater fish species in Korea, for the mining of expressed sequence tags (ESTs). Randomized and non-normalized EST analysis was performed with 7 unidirectional cDNA libraries generated from brain, intestine, kidney, liver, muscle, ovary or testis. Of 3,383 ESTs in total, the number of singleton was 2,029, and 333 contigs containing 1,354 ESTs were assembled (percent of unigene = 70.0%). Abundantly expressed gene transcripts and broad clustering of putative gene function were tissue-specific in general, and the redundancy was also variable among those libraries. Over half of H. mylodon ESTs were matched with orthologues from other teleosts among which zebrafish gene sequences were the most frequent in those matches. This initial setting of EST libraries achieved in the present study would be a fundamental basis for the banking of gene resources from this endangered fish species.