Journal of Aquaculture (한국양식학회지)

The Korean Society of Fisheries and Aquatic Science (한국양식학회)
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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 (Department of Marine Biotechnology, Soonchunhyang University) ;
  • Lim, Yoon-Hee (Department of Marine Biotechnology, Soonchunhyang University) ;
  • Cho, Young-Sun (Department of Aquaculture, Pukyong National University) ;
  • Lee, Sang-Yoon (Department of Aquaculture, Pukyong National University) ;
  • Nam, Yoon-Kwon (Department of Aquaculture, Pukyong National University)
  • Published : 2007.12.31
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Abstract

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.

멸종위기 천연기념물 어류 어름치(Hemibarbus mylodon)를 대상으로한 어름치 유전자 은행 구축 연구의 일환으로 뇌, 소화관, 근육, 간, 신장, 난소 및 정소 조직으로부터 expressed sequence tag (EST) library들을 구축하고 발현 유전자의 탐색을 실시하였다. EST 탐색을 통해 총 3,383개의 발현 유전자 염기서열 단편을 확보하였고 이들로부터 1,354개의 EST를 포함하는 총 333개의 contig들이 형성됨으로써 비교적 높은 빈도(69.8%)의 unigene 확보율을 나타내었다. EST의 조직 별 출현 양상은 orthologue들과의 상동성 정도 및 유추 기능의 대분류를 기준으로 분석할 때 각 조직들은 서로 다른 특징을 나타내었다. 어름치에서 발굴된 EST들은 zebrafish의 유전자들과 가장 높은 match 빈도를 나타내었다. 본 연구를 통해 확보된 EST library들과 염기서열 정보는 본 종의 장외 복원을 위한 효율적인 인공증식 기술 개발에 유용한 기초 정보로 활용될 수 있을 것이다.

Keywords

References

  1. Adams, M. D., J. M. Kelley, J. D. Gocayne, M. Dubnick, M. H. Polymeropoulos, H. Xiao, C. R. Merril, A. Wu, B. Olde, R. F. Moreno, A. R. Kerlavage, W. R. McCombie and J. C. Venter, 1991. Complementary DNA sequencing: expressed sequence tags and human genome project. Science, 252, 1651-1656 https://doi.org/10.1126/science.2047873
  2. Byeon, H.-K., J.-S. Choi, S. R. Jeon, J.-K. Choi and B.-Y. Song, 1996. Fish fauna in the streams of Mt. Chiak. Korean J. Environ. Biol., 14, 47-54
  3. Cho, Y.S., S. Y. Lee, I. C. Bang, D. S. Kim and Y. K. Nam, 2006. Transcriptional response of major antioxidant enzyme genes to heat stress in mud loach (Misgurnus mizolepis). J. Aquacult., 19, 157-165
  4. Douglas, S.E., L.C. Knichkle, J. Kimball and M. Reith, 2007. Comprehensive EST analysis of Atlantic halibut (Hippglossus hippoglossus), a commercially relevant aquaculture species. BMC Genomics, 8, 144 https://doi.org/10.1186/1471-2164-8-144
  5. Douglas, S.E., J. W. Gallant, C. E. Bullerwel, C, Wolff, J. Munholland and M. E. Reith, 1999. Winter flounder expressed sequence tags: establishment of an EST database and identification of novel fish genes. Mar. Biotechnol., 1, 458-464 https://doi.org/10.1007/PL00011802
  6. Gong, Z., T. Yan, J. Liao, S. E. Lee, J. He and C. L. Hew, 1997. Rapid identification and isolation of zebrafish cDNA clones. Gene, 201, 87-98 https://doi.org/10.1016/S0378-1119(97)00431-9
  7. Jang, M.-H., M. C. Lucas and G.-J. Joo, 2003. The fish fauna of mountain streams in South Korean national parks and its significance to conservation of regional freshwater fish biodiversity. Biol. Conserv., 114, 115-126 https://doi.org/10.1016/S0006-3207(03)00016-8
  8. Jenny, M. J., A. H. Ringwood, E. R. Lacy, A. J. Lewitus, J. W. Kempton, P. S. Gross, G. W. Warr and R. W. Chapman, 2002. Potential indicators of stress response identified by expressed sequence tag analysis of hemocytes and embryos from the American oyster, Crassostrea virginica. Mar. Biotechnol., 4, 81-93 https://doi.org/10.1007/s10126-001-0072-8
  9. Kim, K. Y., S. Y. Lee, Y. S. Cho, I. C. Bang, D. S. Kim and Y. K. Nam, 2007. Characterization and phylogeny of two betacytoskeletal actins from Hemibarbus mylodon (Cyprinidae, Cypriniformes), a threatened fish species in Korea. DNA Seq. DOI: 10.1080/10425170701445691
  10. Kono, T, M. Sakai and S. E. LaPatra, 2000. Expressed sequence tag analysis of kidney and gill tissues from rainbow trout Oncorhynchus mykiss infected with infectious hematopoietic necrosis virus. Mar. Biotechnol., 2, 493-498
  11. Lee, Y. H., J. K. Noh, K. Y. Kim, Y. S. Cho, Y. K. Nam and D. S. Kim, 2007. Characterization of mud loach (Misgurnus mizolepis) Apolipoprotein A-I: cDNA cloning, molecular phylogeny and expression analysis. J. Aquacult., 20, 65-72
  12. Liu, X., H. Wang, and Z. Gong, 2006. Tandem-repeated zebrafish zp3 genes possess oocyte-specific promoters and are insensitive to estrogen induction. Biol. Reprod., 74, 1016-1025 https://doi.org/10.1095/biolreprod.105.049403
  13. Marra, M. A., L. Hiller and R. H. Waterston, 1998. Expressed sequence tags-ESTablishing bridges between genomes. Trends Genet., 14, 4-7 https://doi.org/10.1016/S0168-9525(97)01355-3
  14. Moutou, K. A., S. Socorro, D. M. Power, Z. Mamuris and A. V. Canario, 2001. Molecular cloning and sequence of gilthead sea bream (Sparus aurata) alpha-skeletal actin: tissue and developmental expression. Comp. Biochem. Physiol., 130B, 13-21
  15. Savan, R. and M. Sakai, 2002. Analysis of expressed sequence tags EST obtained from common carp, Cyprinus carpio L., head kidney cells after stimulation by two mitogens, lipopolysaccharide and concanavalin-A. Comp. Biochem. Physiol., 131, 71-82
  16. Serapion. J., H. Kucuktas, J. Feng and Z. Liu, 2004. Bioinformatic mining of type I microsatellites from expressed sequence tags of channel catfish (Ictalurus punctatus). Mar. Biotechnol., 6, 364-377 https://doi.org/10.1007/s10126-003-0039-z
  17. Suarez-Castillo, E. C. and J. E. Garcia-Arraras, 2007. Molecular evolution of the ependymin protein family: a necessary update. BMC Evol. Biol., 7, 23
  18. Suarez-Castillo, E. C., W. E. Medina-Ortiz, J. L. Roig-Lopez and J. E. Garcia-Arraras, 2004. Ependymin, a gene involved in regeneration and neroplasticity in vertebrates, is overexpressed uring regeneration in the echinoderm, Holothuria glaberrima. Gene, 334, 1333-1343
  19. Venkatesh, B. and S. Brenner, 1998. Genomic structure and sequence of the pufferfish (Fugu rubripes) gene encoding an actin-related protein. Gene, 211, 169-175 https://doi.org/10.1016/S0378-1119(98)00096-1
  20. Venkatesh, B., B. H. Tay, G. Elgar and S. Brenner, 1996. Isolation, characterization and evolution of nine pufferfish (Fugu rubripes) actin genes. J. Mol. Biol., 259, 655-665 https://doi.org/10.1006/jmbi.1996.0347
  21. Wang, H. and Z. Gong, 1999. Characterization of two zebrafish cDNA eclones encoding egg envelop proteins ZP2 and ZP3. Biochim. Biophys. Acta., 1446. 156-160 https://doi.org/10.1016/S0167-4781(99)00066-4
  22. Zheng, S. and Z. Gong, 2002. Expressed sequence tag analysis of expression profiles of zebrafish testis and ovary. Gene, 294, 45-53 https://doi.org/10.1016/S0378-1119(02)00791-6