메뉴 건너뛰기




Volumn 6, Issue 4, 2014, Pages 807-811

Deep sequencing of the transcriptome and mining of single nucleotide polymorphisms (SNPs) provide genomic resources for applied studies in Chinook salmon (Oncorhynchus tshawytscha)

Author keywords

Chinook salmon; Single nucleotide polymorphisms; Transcriptome assembly; Transcriptome sequencing

Indexed keywords

ONCORHYNCHUS TSHAWYTSCHA; SALMONIDAE;

EID: 84919935488     PISSN: 18777252     EISSN: 18777260     Source Type: Journal    
DOI: 10.1007/s12686-014-0235-3     Document Type: Article
Times cited : (6)

References (21)
  • 1
    • 77956972497 scopus 로고    scopus 로고
    • Multiple PAR and E4BP4 bZIP transcription factors in zebrafish: diverse spatial and temporal expression patterns
    • COI: 1:CAS:528:DC%2BC3cXhtFOktb%2FK, PID: 20854132
    • Ben-Moshe Z, Vatine G, Alon S, Tovin A, Mracek P, Foulkes NS, Gothilf Y (2010) Multiple PAR and E4BP4 bZIP transcription factors in zebrafish: diverse spatial and temporal expression patterns. Chronobiol Int 27:1509–1531
    • (2010) Chronobiol Int , vol.27 , pp. 1509-1531
    • Ben-Moshe, Z.1    Vatine, G.2    Alon, S.3    Tovin, A.4    Mracek, P.5    Foulkes, N.S.6    Gothilf, Y.7
  • 2
    • 79751509492 scopus 로고    scopus 로고
    • Short reads and nonmodel species: exploring the complexities of next-generation sequence assembly and SNP discovery in the absence of a reference genome
    • PID: 21429166
    • Everett MV, Grau ED, Seeb JE (2011) Short reads and nonmodel species: exploring the complexities of next-generation sequence assembly and SNP discovery in the absence of a reference genome. Mol Ecol Resour 11:93–108. doi:10.1111/j.1755-0998.2010.02969.x
    • (2011) Mol Ecol Resour , vol.11 , pp. 93-108
    • Everett, M.V.1    Grau, E.D.2    Seeb, J.E.3
  • 3
    • 84859892361 scopus 로고    scopus 로고
    • Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas
    • COI: 1:CAS:528:DC%2BC38XlvFyltrg%3D
    • Gavery MR, Roberts SB (2012) Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas. Comp Biochem Physiol D Genomics Proteomics 7:94–99. doi:10.1016/j.cbd.2011.12.003
    • (2012) Comp Biochem Physiol D Genomics Proteomics , vol.7 , pp. 94-99
    • Gavery, M.R.1    Roberts, S.B.2
  • 4
    • 33749189435 scopus 로고    scopus 로고
    • Updated status of federally listed ESUs of West Coast salmon and steelhead
    • Dept, Commer:
    • Good TP, Waples RS, Adams PB (2005) Updated status of federally listed ESUs of West Coast salmon and steelhead. U.S. Dept. Commer
    • (2005) U.S
    • Good, T.P.1    Waples, R.S.2    Adams, P.B.3
  • 5
    • 66349087005 scopus 로고    scopus 로고
    • Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery
    • PID: 19402907
    • Hale MC, McCormick CR, Jackson JR, DeWoody JA (2009) Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery. BMC Genomics 10:203. doi:10.1186/1471-2164-10-203
    • (2009) BMC Genomics , vol.10 , pp. 203
    • Hale, M.C.1    McCormick, C.R.2    Jackson, J.R.3    DeWoody, J.A.4
  • 6
    • 77953475815 scopus 로고    scopus 로고
    • Discovery and evaluation of candidate sex-determining genes and xenobiotics in the gonads of lake sturgeon (Acipenser fulvescens)
    • COI: 1:CAS:528:DC%2BC3cXntVCrs7k%3D, PID: 20386959
    • Hale MC, Jackson JR, DeWoody JA (2010) Discovery and evaluation of candidate sex-determining genes and xenobiotics in the gonads of lake sturgeon (Acipenser fulvescens). Genetica 138:745–756. doi:10.1007/s10709-010-9455-y
    • (2010) Genetica , vol.138 , pp. 745-756
    • Hale, M.C.1    Jackson, J.R.2    DeWoody, J.A.3
  • 7
    • 0002051540 scopus 로고    scopus 로고
    • BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT
    • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. In: Nucleic acids symposium series, vol 41, pp 95–98
    • (1999) Nucleic acids symposium series , vol.41 , pp. 95-98
    • Hall, T.A.1
  • 8
    • 67650721347 scopus 로고    scopus 로고
    • CateGOrizer: a web-based program to batch analyze gene ontology classification categories
    • Hu ZL, Bao J, Reecy JM (2008) CateGOrizer: a web-based program to batch analyze gene ontology classification categories. Online J Bioinform 9:108–112
    • (2008) Online J Bioinform , vol.9 , pp. 108-112
    • Hu, Z.L.1    Bao, J.2    Reecy, J.M.3
  • 9
    • 78650159987 scopus 로고    scopus 로고
    • The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing
    • PID: 21087448
    • Jeukens J, Renaut S, St-Cyr J, Nolte AW, Bernatchez L (2010) The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing. Mol Ecol 19:5389–5403. doi:10.1111/j.1365-294X.2010.04934.x
    • (2010) Mol Ecol , vol.19 , pp. 5389-5403
    • Jeukens, J.1    Renaut, S.2    St-Cyr, J.3    Nolte, A.W.4    Bernatchez, L.5
  • 10
    • 84877066818 scopus 로고    scopus 로고
    • Transcriptome-wide comparison of sequence variation in divergent ecotypes of kokanee salmon
    • Lemay MA, Donnelly DJ, Russello MA (2013) Transcriptome-wide comparison of sequence variation in divergent ecotypes of kokanee salmon. BMC Genomics 14. doi:10.1186/1471-2164-14-308
    • (2013) BMC Genomics , pp. 14
    • Lemay, M.A.1    Donnelly, D.J.2    Russello, M.A.3
  • 12
    • 0004152898 scopus 로고    scopus 로고
    • Status review of Chinook salmon from Washington, Idaho, Oregon, and California. U.S. Dept. Commer., NOAA Tech. Memo
    • Myers JM et al. (1998) Status review of Chinook salmon from Washington, Idaho, Oregon, and California. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-35
    • (1998) NMFS-NWFSC-35
    • Myers, J.M.1
  • 13
    • 77957280940 scopus 로고    scopus 로고
    • Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire
    • PID: 20923558
    • Quinn N et al (2010) Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire. BMC Genomics 11:539
    • (2010) BMC Genomics , vol.11 , pp. 539
    • Quinn, N.1
  • 14
    • 84911977440 scopus 로고    scopus 로고
    • R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria
    • R Development Core Team (2010) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, http://www.R-project.org
    • (2010) ISBN 3-900051-07-0
    • Development Core Team, R.1
  • 15
    • 84919884973 scopus 로고    scopus 로고
    • RepeatMasker Open-3.0 (2010) Institute for Systems Biology
    • RepeatMasker Open-3.0 (2010) Institute for Systems Biology. http://www.repeatmasker.org
  • 16
    • 84857550272 scopus 로고    scopus 로고
    • Development of genomic resources for Pacific herring through targeted transcriptome pyrosequencing
    • Roberts SB, Hauser L, Seeb LW, Seeb JE (2012) Development of genomic resources for Pacific herring through targeted transcriptome pyrosequencing. PloS One 7. doi:10.1371/journal.pone.0030908
    • (2012) PloS One , pp. 7
    • Roberts, S.B.1    Hauser, L.2    Seeb, L.W.3    Seeb, J.E.4
  • 17
    • 71949101266 scopus 로고    scopus 로고
    • Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library
    • Sanchez C, Smith T, Wiedmann R, Vallejo R, Salem M, Yao J, Rexroad C (2009) Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library. BMC Genomics 10:559. doi:10.1186/1471-2164-10-559
    • (2009) BMC Genomics , vol.10 , pp. 559
    • Sanchez, C.1    Smith, T.2    Wiedmann, R.3    Vallejo, R.4    Salem, M.5    Yao, J.6    Rexroad, C.7
  • 18
    • 84858150876 scopus 로고    scopus 로고
    • Generation of a reference transcriptome for evaluating rainbow trout responses to various stressors
    • COI: 1:CAS:528:DC%2BC38Xls1Gitrg%3D, PID: 22188770
    • Sanchez CC, Weber GM, Gao GT, Cleveland BM, Yao JB, Rexroad CE (2011) Generation of a reference transcriptome for evaluating rainbow trout responses to various stressors. BMC Genomics 12:626. doi:10.1186/1471-2164-12-626
    • (2011) BMC Genomics , vol.12 , pp. 626
    • Sanchez, C.C.1    Weber, G.M.2    Gao, G.T.3    Cleveland, B.M.4    Yao, J.B.5    Rexroad, C.E.6
  • 19
    • 79751513975 scopus 로고    scopus 로고
    • Transcriptome sequencing and high-resolution melt analysis advance single nucleotide polymorphism discovery in duplicated salmonids
    • COI: 1:CAS:528:DC%2BC3MXks1Kiu78%3D, PID: 21429141
    • Seeb JE, Pascal CE, Grau ED, Seeb LW, Templin WD, Harkins T, Roberts SB (2011) Transcriptome sequencing and high-resolution melt analysis advance single nucleotide polymorphism discovery in duplicated salmonids. Mol Ecol Resour 11:335–348. doi:10.1111/j.1755-0998.2010.02936.x
    • (2011) Mol Ecol Resour , vol.11 , pp. 335-348
    • Seeb, J.E.1    Pascal, C.E.2    Grau, E.D.3    Seeb, L.W.4    Templin, W.D.5    Harkins, T.6    Roberts, S.B.7
  • 20
    • 41149167170 scopus 로고    scopus 로고
    • Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing
    • COI: 1:CAS:528:DC%2BD1cXmtFyitbw%3D, PID: 18266620
    • Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, Marden JH (2008) Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol 17:1636–1647. doi:10.1111/j.1365-294X.2008.03666.x
    • (2008) Mol Ecol , vol.17 , pp. 1636-1647
    • Vera, J.C.1    Wheat, C.W.2    Fescemyer, H.W.3    Frilander, M.J.4    Crawford, D.L.5    Hanski, I.6    Marden, J.H.7
  • 21
    • 84897630238 scopus 로고    scopus 로고
    • So, you want to use next-generation sequencing in marine systems? Insight from the Pan-Pacific Advanced Studies Institute
    • Willette DA et al (2014) So, you want to use next-generation sequencing in marine systems? Insight from the Pan-Pacific Advanced Studies Institute. Bull Mar Sci 90:79–122. doi:10.5343/bms.2013.1008
    • (2014) Bull Mar Sci , vol.90 , pp. 79-122
    • Willette, D.A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.