RNA deep sequencing of the Atlantic cod transcriptome

Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics

Volumn 6, Issue 1, 2011, Pages 18-22

  Johansen, Steinar D ^a,b   Karlsen, Bård Ove ^a,b   Furmanek, Tomasz ^c   Andreassen, Morten ^b   Jørgensen, Tor Erik ^a   Bizuayehu, Teshome T ^a   Breines, Ragna ^b   Emblem, Åse ^b   Kettunen, Päivi ^c   Luukko, Keijo ^c   Edvardsen, Rolf B ^d   Nordeide, Jarle T ^a   Coucheron, Dag H ^b   Moum, Truls ^a  

^a NORD UNIVERSITY   (Norway)

^b UNIVERSITY OF TROMSØ   (Norway)

^c UNIVERSITY OF BERGEN   (Norway)

^d INSTITUTE OF MARINE RESEARCH   (Norway)

Author keywords

Aquaculture; Atlantic cod; Gadus morhua; Genomics; MicroRNA; Next generation sequencing; RNA; Transcriptome

Indexed keywords

MICRORNA; TRANSCRIPTOME;

ANIMAL TISSUE; AQUACULTURE; ATLANTIC COD; CONFERENCE PAPER; DEVELOPMENTAL STAGE; EMBRYO; FISH GENETICS; GENE EXPRESSION PROFILING; GENE SEQUENCE; GENETIC ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PYROSEQUENCING; RNA SEQUENCE; RNA TRANSCRIPTION;

GADUS MORHUA;

EID: 79251606035     PISSN: 1744117X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbd.2010.04.005     Document Type: Conference Paper

References (39)

1. W.J. Ansorge Next-generation DNA sequencing techniques New Biotechnol. 25 2009 195 203
2. Y.W. Asmann, M.B. Wallace, and E.A. Thompson Transcriptome profiling using next-generation sequencing Gastroenterology 135 2008 1466 1468
3. R.W. Carthew, and E.J. Sontheimer Origins and mechanisms of miRNAs and siRNAs Cell 136 2009 642 655
4. J. Cavaillé, K. Buiting, M. Kiefmann, M. Lalande, C.I. Brannan, B. Horsthemke, J.P. Bachellerie, J. Brosius, and A. Hüttenhofer Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization Proc. Natl Acad. Sci. USA 97 2000 14311 14316
5. P.Y. Chen, H. Manninga, K. Slanchev, M. Chien, J.J. Russo, J. Ju, R. Sheridan, B. John, D.S. Marks, D. Gaidatzis, C. Sander, M. Zavolan, and T. Tuschi The developmental miRNA profiles of zebrafish as determined by small RNA cloning Genes Dev. 19 2005 1288 1293
6. F.F. Costa Non-coding RNAs: lost in translation? Gene 386 2007 1 10
7. W.A. Decatur, and M.J. Fournier RNA-guided nucleotide modification of ribosomal and other RNAs J. Biol. Chem. 278 2003 695 698
8. C. Ender, A. Krek, M.R. Friedländer, M. Beitzinger, L. Weinmann, W. Chen, S. Pfeffer, N. Rajewsky, and G. Meister A human snoRNA with microRNA-like functions Mol. Cell 32 2008 519 528
9. A.R. Forrest, and P. Carninci Whole genome transcriptome analysis RNA Biol. 6 2009 107 112
10. A.J. Giraldez, Y. Mishima, J. Rihel, R.J. Grocock, S.V. Dongen, K. Inoue, A.J. Enright, and A.F. Schier Zebrafish miR-430 promotes deadenylation and clearance of maternal mRNAs Science 312 2006 75 79
11. T.R. Gregory, J.A. Nicol, H. Tamm, B. Kullmann, K. Kullmann, I.J. Leitch, B.G. Murray, D.F. Kapraun, J. Greilhuber, and M.D. Bennett Eukaryotic genome size database Nucleic Acids Res. 35 2006 D332 D338
12. S. Griffiths-Jones, H.K. Saini, S. van Dongen, and A.J. Enright miRBase: tools for microRNA genomics Nucleic Acids Res. 36 2008 D154 D158
13. T.E. Hall, P. Smith, and I.A. Johnston Stages of embryonic development in the Atlantic cod Gadus morhua J. Morphol. 259 2004 255 270
14. S. Johansen, and I. Bakke The complete mitochondrial DNA sequence of Atlantic cod (Gadus morhua): relevance to taxonomic studies among codfishes Mol. Mar. Biol. Biotechnol. 5 1996 203 214
15. S.D. Johansen, D.H. Coucheron, M. Andreassen, B.O. Karlsen, T. Furmanek, T.E. Jørgensen, Å. Emblem, R. Breines, J.T. Nordeide, T. Moum, A.J. Nederbragt, N.C. Stenseth, and K.S. Jakobsen Large-scale sequence analyses of Atlantic cod New Biotechnol. 25 2009 263 271
16. P. Kapranov, A.T. Willingham, and T.R. Gingeras Genome-wide transcription and the implications for genomic organization Nature Rev. Genet. 8 2007 413 423
17. T. Kiss Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions Cell 109 2002 145 148
18. W.P. Kloosterman, F.A. Steinar, E. Berezikov, E. de Bruijn, J. van der Belt, M. Verheul, E. Cuppen, and R.H. Plasterk Cloning and expression of new microRNAs from zebrafish Nucleic Acids Res. 34 2006 2558 2569
19. H. Ledford The death of microarrays? Nature 455 2008 847
20. X.-h. Liang, Q. Liu, and M.J. Fournier Loss of rRNA modifications in the decoding center of the ribosome impairs translation and strongly delays pre-rRNA processing RNA 15 2009 1716 1728
21. T.M. Lowe, and S.R. Eddy A computational screen for methylation guide snoRNAs in yeast Science 283 1999 1168 1171
22. E.R. Mardis Next-generation DNA sequencing methods Annu. Rev. Genome. Human Genet. 9 2008 387 402
23. A.G. Matera, R.M. Terns, and M.P. Terns Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs Mol. Cell. Biol. 8 2007 209 220
24. M.L. Metzker Sequencing technologies-the next generation Nat. Rev. Genet. 11 2010 31 46
25. T. Moen, B. Hayes, F. Nilsen, M. Dalghandi, K.T. Fjalestad, S.-E. Fevolden, P.R. Berg, and S. Lien Identification and characterization of novel SNP markers in Atlantic cod: evidence for directional selection BMC Genetics 9 2008 18
26. G.E. Morris The Cajal body Biochim. Biophys. Acta 1783 2008 2108 2115
27. L. Pariset, G. Chillemi, S. Bongiorni, V. Romano Spica, and A. Valetini Microarrays and high-throughput transcriptomic analysis in species with incomplete availability of genomic sequences New Biotechnol. 25 2009 272 279
28. E. Peatman, and Z. Liu Microarray fundamentals: basic principles and application in aquaculture Z. Liu, Aquaculture Genome Technologies, Chapt. 21 2007 Blackwell Publishing 355 368
29. J.C.R. Politz, E.M. Hogan, and T. Pederson MicroRNAs with a nucleolar location RNA 15 2009 1705 1715
30. J.M. Rothberg, and J.H. Leamon The development and impact of 454 sequencing Nat. Biotechnol. 26 2008 1117 1124
31. P. Schattner, W.A. Decatur, C. Davis, M. Ares, M.J. Fournier, and T.M. Lowe Genome-wide searching for pseuduridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome Nucleic Acids Res. 32 2004 4281 4296
32. A.R. Soares, P.M. Pereira, B. Santos, C. Egas, A.C. Gomes, J. Arrajs, J.L. Oliveira, G.R. Moura, and M.A. Santos Parallel DNA pyrosequencing unveils new zebrafish microRNAs BMC Genomics 10 2009 195
33. R.J. Taft, E.A. Glazov, T. Lassmann, Y. Hayashizaki, P. Carninci, and J.S. Mattick Small RNAs derived from snoRNAs RNA 15 2009 1233 1240
34. F. Tang, C. Barbacioru, Y. Wang, E. Nordman, C. Lee, N. Xu, X. Wang, J. Bodeau, B.B. Tuch, A. Siddiqui, K. Lao, and M.A. Surani mRNA-Seq whole-transcriptome analysis of a single cell Nat. Methods 6 2009 377 382
35. E.J. Thatcher, J. Bond, I. Paydar, and J.G. Patton Genomic organization of zebrafish microRNAs BMC Genomics 9 2008 253
36. M.C. Wahl, C.L. Wili, and R. Luhrmann The spliceosome: design principles of a dynamic RNP machine Cell 136 2009 701 718
37. Z. Wang, M. Gerstein, and M. Snyder RNA-Seq: a revolutionary tool for transcriptomics Nat. Rev. Genet. 10 2009 57 63
38. J.H. Yang, X.C. Zhang, Z.P. Huang, H. Zhou, M.B. Huang, S. Zhang, Y.Q. Chen, and L.H. Qu snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome Nucleic Acids Res. 34 2006 5112 5123
39. Y. Zhang, J. Liu, C. Jia, T. Li, R. Wu, J. Wang, Y. Chen, X. Zou, R. Chen, X.-J. Wang, and D. Zhu Systematic identification and evolutionary features of rhesus monkey small nucleolar RNAs BMC Genomics 11 2010 61