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Vol. 102, No. 1-4, 2003
Issue release date: 2003
Cytogenet Genome Res 102:347–354 (2003)
(DOI:10.1159/000075773)

Sequence analysis of a rainbow trout cDNA library and creation of a gene index

Rexroad III C.E. · Lee Y. · Keele J.W. · Karamycheva S. · Brown G. · Koop B. · Gahr S.A. · Palti Y. · Quackenbush J.
aUSDA/ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, West Virginia; bRoman L. Hruska USDA/ARS Meat Animal Research Center, Clay Center, Nebraska; cThe Institute for Genomic Research, Rockville, Maryland (USA); dCenter for Biomedical Research, University of Victoria, Victoria, British Columbia (Canada); eDepartment of Biochemistry, The George Washington University, Washington, DC (USA)

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Abstract

Expressed sequence tag (EST) projects have produced extremely valuable resources for identifying genes affecting phenotypes of interest. A large-scale EST sequencing project for rainbow trout was initiated to identify and functionally annotate as many unique transcripts as possible. Over 45,000 5′ ESTs were obtained by sequencing clones from a single normalized library constructed using mRNA from six tissues. The production of this sequence data and creation of a rainbow trout Gene Index eliminating redundancy and providing annotation for these sequences will facilitate research in this species.   



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References

  1. Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiaol H, Merril CR, Wu A, Olde B, Moreno RF, et al: Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252:1651–1656 (1991).
  2. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, Gabor GL, Abril JF, Agbayani A, An HJ, Andrews-Pfannkoch C, Baldwin D, Ballew RM, Basu A, Baxendale J, Bayraktaroglu L, Beasley EM, Beeson KY, Benos PV, Berman BP, Bhandari D, Bolshakov S, Borkova D, Botchan MR, Bouck J, Brokstein P, Brottier P, Burtis KC, Busam DA, Butler H, Cadieu E, Center A, Chandra I, Cherry JM, Cawley S, Dahlke C, Davenport LB, Davies P, de Pablos B, Delcher A, Deng Z, Mays AD, Dew I, Dietz SM, Dodson K, Doup LE, Downes M, Dugan-Rocha S, Dunkov BC, Dunn P, Durbin KJ, Evangelista CC, Ferraz C, Ferriera S, Fleischmann W, Fosler C, Gabrielian AE, Garg NS, Gelbart WM, Glasser K, Glodek A, Gong F, Gorrell JH, Gu Z, Guan P, Harris M, Harris NL, Harvey D, Heiman TJ, Hernandez JR, Houck J, Hostin D, Houston KA, Howland TJ, Wei MH, Ibegwam C, Jalali M, Kalush F, Karpen GH, Ke Z, Kennison JA, Ketchum KA, Kimmel BE, Kodira CD, Kraft C, Kravitz S, Kulp D, Lai Z, Lasko P, Lei Y, Levitsky AA, Li J, Li Z, Liang Y, Lin X, Liu X, Mattei B, McIntosh TC, McLeod MP, McPherson D, Merkulov G, Milshina NV, Mobarry C, Morris J, Moshrefi A, Mount SM, Moy M, Murphy B, Murphy L, Muzny DM, Nelson DL, Nelson DR, Nelson KA, Nixon K, Nusskern DR, Pacleb JM, Palazzolo M, Pittman GS, Pan S, Pollard J, Puri V, Reese MG, Reinert K, Remington K, Saunders RD, Scheeler F, Shen H, Shue BC, Siden-Kiamos I, Simpson M, Skupski MP, Smith T, Spier E, Spradling AC, Stapleton M, Strong R, Sun E, Svirskas R, Tector C, Turner R, Venter E, Wang AH, Wang X, Wang ZY, Wassarman DA, Weinstock GM, Weissenbach J, Williams SM, WoodageT, Worley KC, Wu D, Yang S, Yao QA, Ye J, Yeh RF, Zaveri JS, Zhan M, Zhang G, Zhao Q, Zheng L, Zheng XH, Zhong FN, Zhong W, Zhou X, Zhu S, Zhu X, Smith HO, Gibbs RA, Myers EW, Rubin GM, Venter JC: The genome sequence of Drosophila melanogaster. Science 287:2185–2195 (2000).
  3. Allendorf FW, Thorgaard GH: Tetraploidy and the evolution of salmonid fishes, in Turner BJ (ed): Evolutionary Genetics of Fishes, pp 1–46 (Plenum Press, New York 1984).
  4. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J molec Biol 215:403–410 (1990).
  5. Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, Gelpke MD, Roach J, Oh T, Ho IY, Wong M, Detter C, Verhoef F, Predki P, Tay A, Lucas S, Richardson P, Smith SF, Clark MS, Edwards YJ, Doggett N, Zharkikh A, Tavtigian SV, Pruss D, Barnstead M, Evans C, Baden H, Powell J, Glusman G, Rowen L, Hood L, Tan YH, Elgar G, Hawkins T, Venkatesh B, Rokhsar D, Brenner S: Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297:1301–1310 (2002).
  6. Collins FS: Positional cloning moves from perditional to traditional. Nature Genet 9:347–350 (1995).
  7. Danzmann RG, Jackson TR, Ferguson MM: Epistasis in allelic expression at upper temperature tolerance QTL in rainbow trout. Aquaculture 173:45–58 (1999).
  8. Huang X, Madan A: CAP3: A DNA sequence assembly program. Genome Res 9:868–877 (1999).
  9. Huang X, Adams MD, Zhou H, Kerlavage AR: A tool for analyzing and annotating genomic sequences. Genomics 46:37–45 (1997).
  10. Jackson TR, Ferguson MM, Danzmann RG. Fishback AG, Ihssen PE, O’Connel M, Crease TJ: Identification of two QTL influencing upper temperature tolerance in three rainbow trout (Oncorhynchus mykiss) half-sib families. Heredity 80:143–151 (1998).
  11. Katagiri T, Asakawa S, Minagawa, S, Shimizu N, Hirono I, Aoki T: Construction and characterization of BAC libraries for three fish species; rainbow trout, carp and tilapia. Anim Genet 32:200–204 (2001).
  12. Lander ES, Botstein D: Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199 (1989).
  13. Lee Y, Sultana R, Pertea G, Cho, J, Karamycheva S, Tsai J, Parvizi B, Cheung F, Antonescu V, White J, Holt I, Liang F, Quackenbush J: Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA). Genome Res 12:493–502 (2002).
  14. Nakamura K, Ozaki A, Akutsu T, Iwai K, Sakamoto T, Yoshizaki G, Okamoto N: Genetic mapping of the dominant albino locus in rainbow trout (Oncorhynchus mykiss). Mol Genet Genom 265:687–693 (2001).
  15. Nichols KM, Young WP, Danzmann RG, Robison BD, Rexroad C, Noakes M, Phillips RB, Bentzen P, Spies I, Knudsen K, Allendorf FW, Cunningham BM, Brunelli J, Zhang H, Ristow S, Drew R, Brown KH, Wheeler PA, Thorgaard GH: A consolidated linkage map for rainbow trout (Oncorhynchus mykiss). Anim Genet 34:102–115 (2003).
  16. O’Brien SJ, Womack JE, Lyons LA, Moore KJ, Jenkins NA, Copeland NG: Anchored reference loci for comparative genome mapping in mammals. Nature Genet 3:103–112 (1993).
  17. Ozaki A, Sakamoto T, Khoo S, Nakamura K, Coimbra MRM, Akutsu T, Okamoto N: Quantitative trait loci (QTLs) associated with resistance/susceptibility to infectious pancreatic necrosis virus (IPNV) in rainbow trout (Oncorhynchus mykiss). Mol Genet Genom 265:23–31 (2001).
  18. Perry GML, Danzmann RG, Ferguson MM, Gibson JP: Quantitative trait loci for upper thermal tolerance in outbred strains of rainbow trout (Oncorhynchus mykiss). Heredity 86:333–341 (2001).
  19. Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J: TIGR Gene Indices Clustering Tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19:651–652 (2003).
  20. Quackenbush J, Cho J, Lee D, Liang F, Holt I, Karamycheva S, Parvizi B, Pertea G, Sultana R, White J: The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucl Acid Res 29:159–164 (2001).
  21. Robison BD, Wheeler PA, Sundin K, Sikka P, Thorgaard GH: Composite interval mapping reveals a major locus influencing embryonic development rate in rainbow trout (Oncorhynchus mykiss). J Hered 92:16–22 (2001).
  22. Sakamoto T, Danzmann RG, Okamoto N, Ferguson MM, Ihssen PE: Linkage analysis of quantitative trait loci associated with spawning time in rainbow trout (Oncorhynchus mykiss). Aquaculture 173:33–43 (1999).
  23. Sakamoto T, Danzmann RG, Gharbi K, Howard P, Ozaki A, Khoo SK, Woram RA, Okamoto N, Ferguson MM, Holm LE, Guyomard R, Hoyheim B: A microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) characterized by large sex-specific differences in recombination rates. Genetics 155:1331–1345 (2000).
  24. Schena, M, Shalon, D, Davis, RW, Brown, PO: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470 (1995).
  25. Soares MB, Bonaldo MDF, Jelene P, Su L, Lawton L, Efstratiadis A: Construction and characterization of a normalized cDNA library. Proc natl Acad Sci, USA 91:9228–9232 (1994).
  26. The Gene Ontology Consortium: Gene ontology: tool for the unification of biology. Nature Genet 25:25–31 (2000).
  27. Thorgaard GH, Bailey GS, Williams D, Buhler DR, Kaattari SL, Ristow SS, Hansen JD, Winton JR, Bartholomew JL, Nagler JJ, Walsh PJ, Vijayan MM, Devlin RH, Hardy RW, Overturf KE, Young WP, Robison BD, Rexroad CE, Palti Y: Status and opportunities for genomics research with rainbow trout. Comp biochem Physiol Part B 133:609–646 (2002).
  28. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigo R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X: The sequence of the human genome. Science 291:1304–1351 (2001).
  29. Young, WP, Wheeler PA, Coryell VH, Keim P, and Thorgaard GH: A detailed genetic linkage map of rainbow trout produced using doubled haploids. Genetics 148:839–850 (1998).
  30. Young WP, Wheeler PA, Fields RD, Thorgaard GH: DNA fingerprinting confirms isogenicity of androgenetically derived rainbow trout lines. J Hered 87:77–81 (1996). Zhang, Z, Schwartz, S, Wagner, L, Miller, W: A greedy algorithm for aligning DNA sequences, J Comput Biol 7:203–214 (2000).


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