Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas

Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics

Volumn 7, Issue 2, 2012, Pages 94-99

  Gavery, MacKenzie R ^a   Roberts, Steven B ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Crassostrea gigas; Environment; Gene expression; Next generation sequencing; Pacific oyster

Indexed keywords

RNA; TRANSCRIPTOME;

ARTICLE; CELL DEATH; CRASSOSTREA GIGAS; DNA SEQUENCE; ENVIRONMENTAL FACTOR; GENE EXPRESSION; GENE IDENTIFICATION; GENE MAPPING; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; IMMUNE RESPONSE; MOLECULAR RECOGNITION; NONHUMAN; OYSTER; PRIORITY JOURNAL; RNA SEQUENCE;

CRASSOSTREA GIGAS;

EID: 84859892361     PISSN: 1744117X     EISSN: 18780407     Source Type: Journal    
DOI: 10.1016/j.cbd.2011.12.003     Document Type: Article

References (40)

1. S.F. Altschul, W. Miller, E.W. Myers, and D.J. Lipman Basic local alignment search tool J. Mol. Biol. 215 1990 403 410
2. K. Baggerly, L. Deng, J. Morris, and C. Aldaz Differential expression in SAGE: accounting for normal between-library variation Bioinformatics 19 2003 1477 1483 (Pubitemid 37038863)
3. D. Blankenberg, G. Von Kuster, N. Coraor, G. Ananda, R. Lazarus, M. Mangan, A. Nekrutenko, and J. Taylor Galaxy: a web-based genome analysis tool for experimentalists Curr. Protoc. Mol. Biol. 19 2010 (Unit 19.10.1-21)
4. J.A. Craft, J.A. Gilbert, B. Temperton, K.E. Dempsey, K. Ashelford, B. Tiwari, T.H. Hutchinson, and J.K. Chipman Pyrosequencing of Mytilus galloprovincialis cDNAs: tissue-specific expression patterns Plos One 5 2010 e8875
5. R. Cullum, O. Alder, and P.A. Hoodless The next generation: using new sequencing technologies to analyse gene regulation Respirology 16 2011 210 222
6. J. de Lorgeril, R. Zenagui, R.D. Rosa, D. Piquemal, and E. Bachère Whole transcriptome profiling of successful immune response to Vibrio infections in the oyster Crassostrea gigas by digital gene expression analysis PLoS One 6 8 2011 e23142
7. J.C. Dohm, C. Lottaz, T. Borodina, and H. Himmelbauer Substantial biases in ultra-short read data sets from high-throughput DNA sequencing Nucleic Acids Res. 36 2008 e105
8. K. Etebari, R. Palfreyman, D. Schlipalius, L. Nielsen, R. Glatz, and S. Asgari Deep sequencing-based transcriptome analysis of Plutella xylostella larvae parasitized by Diadegma semiclausum BMC Genomics 12 2011 446
9. M. Everett, E. Grau, and J. Seeb Short reads and non-model species: exploring the complexities of next generation sequence assembly and SNP discovery in the absence of a reference genome Mol. Ecol. Resour. 11 2011 93 108
10. B. Ewing, and P. Green Base-calling of automated sequencer traces using phred. II. Error probabilities Genome Res. 8 1998 186 194 (Pubitemid 28177230)
11. B. Ewing, L. Hillier, M.C. Wendl, and P. Green Base-calling of automated sequencer traces using phred. I. Accuracy assessment Genome Res. 8 1998 175 185 (Pubitemid 28177229)
12. B. Feldmeyer, C.H. Wheat, N. Krezdorn, B. Rotter, and M. Pfenninger Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance BMC Genomics 12 2011 317
13. E. Fleury, A. Huvet, C. Lelong, J. de Lorgeril, V. Boulo, Y. Gueguen, E. Bachère, A. Tanguy, D. Moraga, C. Fabioux, P. Lindeque, J. Shaw, R. Reinhardt, R. Prunet, G. Davey, S. Lapègue, C. Sauvage, C. Corporeau, J. Moal, F. Gavory, P. Wincker, F. Moreews, C. Klopp, M. Mathieu, P. Boudry, and B. Favrel Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase BMC Genomics 10 2009 341
14. B.A. Fraser, C.J. Weadick, I. Janowitz, H. Rodd, and K.A. Hughes Sequencing and characterization of the guppy (Poecilia reticulata) transcriptome BMC Genomics 12 2011 202
15. J. Goecks, A. Nekrutenko, and J. Taylor The Galaxy Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences Genome Biol. 1 2010 R86
16. F. Goetz, D. Rosauer, S. Sitar, G. Goetz, C. Simchick, S. Roberts, R. Johnson, C. Murphy, C. Bronte, and S. MacKenzie A genetic basis for the phenotypic differentiation between siscowet and lean lake trout (Salvelinus namaycush) Mol. Ecol. 19 2010 176 196
17. Y. Gueguen, J.-P. Cadoret, D. Flament, C. Barreau-Roumiguière, A.-L. Girardot, J. Garnier, A. Horeau, E. Bachère, and J.-M. Escoubas Immune gene discovery by expressed sequence tags generated from hemocytes of the bacteria-challenged oyster, Crassostrea gigas Gene 303 2003 139 145 (Pubitemid 36151778)
18. E. Ha, K. Lee, Y.Y. Seo, S. Kim, J. Lim, B. Oh, J. Kim, and W. Lee Coordination of multiple dual oxidase-regulatory pathways in responses to commensal and infectious microbes in Drosophila gut Nat. Immunol. 10 2009 949 957
19. J.E. Harrison, and J. Schultz Studies on the chlorinating activity of myeloperoxidase J. Biol. Chem. 251 1976 1371 1374
20. E.C. Hoffman, H. Reyes, F.F. Chu, F. Sander, L.H. Conley, B.A. Brooks, and O. Hankinson Cloning of a factor required for activity of the Ah (dioxin) receptor Science 252 1991 954 958 (Pubitemid 21917012)
21. D.W. Huang, B.T. Sherman, and R.A. Lempicki Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists Nucleic Acids Res. 37 2009 1 13
22. D.W. Huang, B.T. Sherman, and R.A. Lempicki Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources Nat. Protoc. 4 2009 44 57
23. M.W. Johansson Cell adhesion molecules in invertebrate immunity Dev. Comp. Immunol. 23 1999 303 315 (Pubitemid 29309609)
24. R. Kawahara-Miki, K. Wada, N. Azuma, and S. Chiba Expression profiling without genome sequence information in a non-model species, pandalid shrimp (Pandalus latirostris), by next-generation sequencing PLoS One 6 10 2011 e26043
25. S. Koutsogiannaki, and M. Kaloyianni Effect of 17β-estradiol on adhesion of Mytilus galloprovincialis hemocytes to selected substrates. Role of alpha2 integrin subunit Fish Shellfish Immunol. 31 2011 73 80
26. I. Lamprou, I. Mamali, K. Dallas, V. Fertakis, M. Lampropoulou, and V.J. Marmaras Distinct signalling pathways promote phagocytosis of bacteria, latex beads and lipopolysaccharide in medfly haemocytes Immunology 121 2007 314 327 (Pubitemid 46817353)
27. Y.C. Lin, C.M. Tayag, C.L. Huang, W.C. Tsui, and J.C. Chen White shrimp Litopenaeus vannamei that had received the hot-water extract of Spirulina platensis showed earlier recovery in immunity and up-regulation of gene expression after pH stress Fish Shellfish Immunol. 29 2010 1092 1098
28. E. Meyer, G. Aglyamova, S. Wang, J. Buchanan-Carter, D. Abrego, J.K. Colbourne, B.L. Willis, and M.V. Matz Sequencing and de novo analysis of a coral larval transcriptome using 454 GS-Flx BMC Genomics 10 2009
29. E. Meyer, M.V. Aglyamova, and G.V. Matz Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure Mol. Ecol. 20 2011 3599 3616
30. A. Mortazavi, B.A. Williams, K. McCue, L. Schaeffer, and B. Wold Mapping and quantifying mammalian transcriptomes by RNA-Seq Nat. Methods 5 2008 585 587
31. J.A. Newton, S.L. Albertson, K.V. Voorhis, C. Maloy, and E. Siegel Washington State Marine Water Quality, 1998 through 2000, Publication #02-03-056 2002 (111pp.)
32. E. Novaes, D.R. Drost, W.G. Farmerie, G.J. Pappas, D. Grattapaglia, R.R. Sederoff, and M. Kirst High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome BMC Genomics 9 2008 312
33. G.I. Rice, J. Bond, A. Asipu, R.L. Brunette, I.W. Manfield, I.M. Carr, J.C. Fuller, R.M. Jackson, T. Lamb, T.A. Briggs, M. Ali, H. Gornall, L.R. Couthard, A. Aeby, S.P. Attard-Montalto, E. Bertini, C. Bodemer, K. Brockmann, L.A. Brueton, P.C. Corry, I. Desguerre, E. Fazzi, A.G. Cazorla, B. Gener, B.C.J. Hamel, A. Heiberg, M. Hunter, M.S. van der Knaap, R. Kumar, L. Lagae, P.G. Landrieu, C.M. Lourenco, D. Marom, M.F. McDermott, W. van der Merwe, S. Orcesi, J.S. Prendiville, M. Rasmussen, S.A. Shalev, D.M. Soler, M. Shinawi, R. Spiegel, T.Y. Tan, A. Vanderver, E.L. Wakeling, E. Wassmer, E. Whittaker, P. Lebon, D.B. Stetson, D.T. Bonthron, and Y.J. Crow Mutations involved in aicardi-goutieres syndrome implicate samhd1 as regulator of the innate immune response Nat. Genet. 41 2009 829 832
34. S.B. Roberts, G. Goetz, S. White, and F. Goetz Analysis of genes isolated from plated hemocytes of the Pacific oysters Crassostrea gigas Mar. Biotechnol. 11 2008 24 44
35. D. Schlenk, P. Garcia Martinez, and D.R. Livingstone Studies on myeloperoxidase activity in the common mussel, Mytilus edulis Comp. Biochem. Physiol. 99C 1991 63 68
36. J.E. Seeb, C.E. Pascal, E.D. Grau, L.W. Seeb, W.D. Templin, S.B. Roberts, and T. Harkins Transcriptome sequencing and high-resolution melt analysis advance SNP discovery in duplicated salmonids Mol. Ecol. Resour. 11 2010 335
37. J. Shendure, and H.L. Ji Next-generation DNA sequencing Nat. Biotechnol. 26 2008 1135 1145
38. J.C. Vera, C.W. Wheat, H.W. Fescemyer, M.J. Frilander, D.L. Crawford, I. Hanski, and J.H. Marden Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing Mol. Ecol. 17 2008 1636 1647 (Pubitemid 351441703)
39. Z. Wang, M. Gerstein, and M. Snyder RNA-Seq: a revolutionary tool for transcriptomics Nat. Rev. Genet. 10 2009 57 63
40. Washington State Department of Health: Office of Shellfish and Protection A Report for the Puget Sound Assessment and Monitoring Program: Atlas of Fecal Coliform Pollution in Puget Sound: Year 2005 2006 (Publication #332-061, 80 pp.)