• Journal of fish pathology
• /
• v.22 no.3
• /
• pp.353-366
• /
• 2009

We constructed a rock bream Oplegnathus fasciatus leukocyte cDNA library and a total of 795 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 795 EST clones, 491 different ESTs showed significant homology to previously described genes while 304 ESTs were unidentified, hypothetical, or unnamed proteins. Encoding 121 different sequences were identified as putative bio-defense genes or genes associated with immune response.

• Journal of Aquaculture
• /
• v.16 no.1
• /
• pp.8-14
• /
• 2003

To generate expressed sequence tags for genomics research involving genetic linkage analysis, to examine gene expression profiles in muscles of channel catfish in a non-normalized muscle cDNA library, to compare gene expression in young and mature channel catfish muscles using the EST reagents and gene filters to demonstrate the feasibility of functional genomics research in small laboratories. 102 randomly picked cDNA clones were analyzed from the catfish muscle cDNA library. Of the sequences generated, 90.2% of ESTs was identified as known genes by identity comparisons. These 92 clones of known gene products represent transcriptional products of 24 genes. The 10 clones of unknown gene products represent 8 genes. The major transcripts (70.1% of the analyzed ESTs) in the catfish muscle are from many major genes involved in muscle contraction, relaxation, energy metabolism and calcium binding such as alpha actin, creatine kinase, parvalbumin, myosin, troponins, and tropomyosins. Gene expression of the unique ESTs was comparatively studied in the young and adult catfish muscles. Significant differences were observed for aldolase, myostatin, myosin light chain, parvalbumin, and an unknown gene. While myosin light chain and an unknown gene (CM 192) are down-regulated in the mature fish muscle, the aldolase, myostatin, and parvalbumin are significantly up-regulated in the mature fish muscle. Although the physiological significance of the changes in expression levels needs to be further addressed, this research demonstrates the feasibility and power of functional genomics in channel catfish. Channel catfish muscle gene expression profiles provide a valuable molecular muscle physiology blueprint for functional comparative genomics.

• Proceedings of the Korean Society of Sericultural Science Conference
• /
• 2003.10a
• /
• pp.144-144
• /
• 2003

In order to understand the expression profile of earthworm midgut, we analyzed 1255 expressed sequence tags (ESTs) derived from earthworm midgut cDNA library. Among 1255 ESTs analyzed, 537 (42.8%) ESTs represented 231 unique genes of which 168 ESTs were singletons and 63 ESTs represented by two or more ESTs. A total of 571 unknown ESTs showed no significant homology. The remaining 147 (11.7%) ESTs whose lengths were less than 150 bp were removed. Among 231 identified unique genes, 168 genes (72.7%) were sequenced only once. (omitted)

• Proceedings of the Korean Society of Life Science Conference
• /
• 2006.09a
• /
• pp.44.1-44.1
• /
• 2006

• Journal of fish pathology
• /
• v.22 no.3
• /
• pp.383-389
• /
• 2009

Analysis of expressed sequence tags (ESTs) is an efficient approach for gene discovery, expression profiling, and development of resources useful for functional genomics studies. As part of studies on the immune system of olive flounder, a total of 251 EST sequences from gill cDNA library were generated to identify and characterize important genes in the immune machanisms of olive flounder. Of the 251 clones, 126 clones (50.2%) were identified as orthologues of known genes from olive flounder and other organisms. Among the 126 EST clones, 16 clones (12.7%) were representing 9 unique genes identified as homologous to the previously reported olive flounder ESTs, 100 clones (79.4%) representing 103unique genes were identified as orthologs of known genes from other organisms. We also identified several kinds of immune associated proteins, indicating EST as a powerful method for identifying immune related 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.

• Proceedings of the Plant Resources Society of Korea Conference
• /
• 2003.04a
• /
• pp.121-121
• /
• 2003

Expressed sequence tags (EST) are help to quickly identify functions of expressed genes and to understand the complexity of gene expression. To assist genetic study of the root development in Panax ginseng, which is one of the most important medicinal plant, expressed sequence tags (EST) analysis was carried out. We constructed a CDNA library using the 4-year Chunpoon root. Partial sequences were obtained from 3,841 clone. The ESTs could be clustered into 2,056 (64%) non-redundant groups. Similarity search of the non-redundant ESTs against public non-redundant databases of both protein and DNA indicated that 1,498 groups show similarity to genes of known function. These ESTs clones were divided into eighteen categories depending upon gene function. The most abundant transcripts were major latex protein (41), ribonuclease 2 (36), metallothionein 2(35). Our extensive EST analysis of genes expressed in 4-year Chunpoong root not only contributes to the understanding of the dynamics of genome expression patterns in root organ development but also adds data to the repertoire of all genomic genes.

• Proceedings of the Korean Aquaculture Society Conference
• /
• 2006.05a
• /
• pp.432-434
• /
• 2006

• The Korea Genome Conference
• /
• 2005.09a
• /
• pp.78-78
• /
• 2005

• Korean Journal of Ichthyology
• /
• v.18 no.4
• /
• pp.283-292
• /
• 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.

• Korean Journal of Ichthyology
• /
• v.19 no.4
• /
• pp.257-265
• /
• 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.