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

  • Nam, Yoon-Kwon (Research Center for Ocean Industrial Development, Pukyang National University) ;
  • Kim, Dong-Soo (Department of Aquaculture, Pukyong National University)
  • Published : 2001.03.01

Abstract

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.

Keywords

References

  1. Science v.252 Complementary DNA sequencing:expressed sequence tags;human genome project Adams;M.D.;J.M.Kelley;J.D.Gocayne;M.Dubnick;M.H.Polymeropolous;H.Xiao;C.R.Merril;A.Wu;B.Olde;R.F.Moreno;A.R.Kerlavage;W.R.McCombie;J.C.Venter
  2. Abstract of Symposium for a Step toward tie Great Future of Aquatic Genomics Differential expression of potential immune response genes in Taura syndrome virus(TSV);white spot virus(WSV)-challenged shrimp. Alcivar-Warren;A
  3. Genc v.180 Sequences of two expressed sequence tags(EST)from rice encoding different cap-binding proteins Aliyeva;E.;A.M.Metz;K.S.Browning
  4. Nucleic Acids Res v.25 Gappled BLAST;PSI-BLAST:a new generation of protein database search programs Altschul;S.F.;T.L.Madden;A.A.Schaffer;J.Zhang;Z.Zhang;W.Miller;D.G.Lipman
  5. Mar.Biotechnol v.1 Sequences of 596 cDNA clones(565,997 bp)of Japanese flounder(Paralichthys olicaceus)leuko-cyes infected with Hirame Rhabdovirus Aoki;T.;B.H.Nam;I.Hirono;E.Yamamoto
  6. Nature Genet v.10 Establishing a human transcript map Boguski;M.S.;G.D.Schuler
  7. Bio Techniques v.21 Automated DNA sequencing requiringno DNA template purification Chen;Q.;C.Neville;A.MacKenzie;R.Korneluk
  8. Abstract of Symposium for a Step toward the Great Future of Aquatic Genomics Expressed sequence tags-a snap-shot of the fish genome Duglas;S.E.
  9. J.Mar.Biotechnol v.6 Isolation of cDNAs for trypsinogen from the winter flounder Pleuronectes americanus Douglas;S.E;J.W.Gallant
  10. Mar.Bioltechnol v.1 Winter flounder expressed sequence tags:establishment of an EST database;identification of novel fish genes Douglas;S.E.;J.W.Gallant;C.E.Bullerwell;C.Wolff;J.Mungolland;M.E.Reith
  11. J.Fish.Biol v.55 Ontogeny of the stomach in winter flounder:characterisation ; expression of the pepsinogen ; proton pump gcnes;determination of pepsin activity Douglas;S.E.;A.Gasulicka;S.Mandla;J.W.Gallant
  12. Pleuronectes americanus.Aquaculture v.190 Molecular analysis of the amylase gene;its expression during development in the winter flounder Doulglas;S.E.;S.Mandla;J.W.Gallant
  13. CAB International Comparison of traditional breeding;transgenesis in farmed fisg with implications for erowth engancement;fitness,Transgenic Animals in Agriculture Dungam;R.A.;R.H.Devlin;Murray J.D.;G.B.Anderson;A.M.Oberbauer;M.N.McGloughlin;(ed.)
  14. Abstract of Symposium for a Step toward the Great Future of Aquatic Genomics Gene mapping,isolation;genetic improvement in catfish Dungam;R.H;Z.Liu
  15. Gene v.201 Rapid identification;isolation of zebrafish cDNA clones Gong;Z.;T.Yan;S.E.Lee;J.He;C.L.Hew
  16. Mol.Mar.Biol.Biotechnol v.3 Bulk isolation;identification of fish genes by cDNA clone tagging Gong;Z.;Z.Hu;Z.Q.Gong;R.Kitching;C.L.Hew
  17. J.Fish Biol v.47 Transgenic salmon:tailoring the genome for food production Hew;C.L.;G.L.Fletcher;P.L.Davies
  18. Mol.Mar.Biol.Biotechnol v.6 Expressed sequence tags of medaka(Oryzias latipes)liver mRNA. Hirono;I;T.Aoki
  19. Mol.Mar.Biol.Biotechnol v.6 Asurvey of expressed genes in Japanese flounder(Paralichthys olivaceus)liver;spleen Inoue;S.;B.H.Nam;I.Hirono;T.Aoki
  20. Mar.Biotechnol v.2 Expressed sequence tag analysis of kidney;gill tissues from rainbow trout(Oncorhynchus mykiss)infected with infectious hematopoietic necrosis virus Kono;T.;M.Sakai;S.E.LaPatra
  21. Mar.Biotechnol v.1 Tissue-specific expressed sequence tags from the black tiger shrimp Penaeus Monodon Lehnert;S.A.;K.J.Wilson;K.Byrne;S.S.Moore
  22. Mar.Biotechnol v.1 Devel-opment of polymorphic EST markers suitable for genetic linkage mapping of catfish. Liu;Z.;A.Karsi;R.A.Dunham
  23. Recent Advance in Marine Biotechnology v.4 Application of biotechnology to enhance growth of salmonids;other fish McLean;E.;R.H.Devlin;Fingerman;M.;R.Nagabhushanam
  24. Recent Advance in Marine Biotechnology v.4 The application of gene manipulation to aquaculture Moav;B;Fingerman;M.;R.Nagabhushanam;(ed.)
  25. Aquacultue(submitted) Isolation;transient expression of a cDNA encoding L-gulono-r-lactone oxidase,a key enzyme for L-ascorbic acidbiosyntheis,from the tiger shark Scyliorhiuns torazame Nam;Y.K.;Y.S.Cho;S.E.Douglas;J.W.Gallant;M.E.Reith;D.S.Kim
  26. Anim.Genet v.27 Development ;mapping of polymorphic microsatellite marers derived from a chicken brain cDNA library Ruyter-Spira;C.P.;R.A.Crooijmans;R.SM.Dijkhof;P.M.Van Oers;J.A.Strijk;J.Van der Poel;M.M.Groenen
  27. Biotechniques v.29 Direct colony sequencing of plasmid DNA by dye terminator methods Saso;C
  28. Abstract of Symposium for a Step toward the Great Future of Aquatic Genomics Oyster genomics:search for sex-determining;growth-regulating genes in the pacific oyster C.Gigas Shimizu;N.;J.Y.Lee;Y.Sato;Y.Shimizu;H.Ohtake;S.Asakawa
  29. Abstract of Symposium for a Step toward the Great Future of Aquatic Genomics Progress in medaka genetics;genomics Shima;A.
  30. Curr.Opin.Genet.Dev v.4 Simple sequences Tautz;D;C.Schlotterer
  31. Abstract of Symposium for a Stip toward tie Great Future of Aquatic Genomics The program in marine genomics in Charleston Warr;G
  32. Naturc Genet v.1 A survey of expressed genes in Caenorhabditis elegans Waterston;R.;C.Martin;M.Craxton;C.Huynh;A.Coulson;L.Hiller;R.Durbin;P.Green;R.Shown-keen;N.Halloran;M.Metzstein;T.Hawkins;R.Wilson;M.Berks;Z.Du;K.Thomas;J.Thierry-Mieg;J.Sulston
  33. Nucleic Acids Res v.25 A comparison of expressed sequence tags(ESTs)to humangenomic sequences Wolfsberg;T.G;D.Landsman