SNP Discovery in Non-model Organisms Using 454 Next Generation Sequencing
DOI: 10.1007/978-1-61779-870-2_3
关键词: Model organism 、 Single-nucleotide polymorphism 、 Computational biology 、 Pyrosequencing 、 DNA sequencing 、 Transcriptome 、 SNP 、 Biology
摘要: Roche 454 sequencing of the transcriptome has become a standard approach for efficiently obtaining single nucleotide polymorphisms (SNPs) in non-model species. In this chapter, primary issues facing development SNPs from species are presented: tissue and sampling choices, mRNA preparation, considerations normalization, pooling barcoding, how much to sequence, assemble data assess assembly, calling SNPs, developing these into genomic publishing work. Discussion also covers comparison RAD-tag potential using other platforms SNP development.
springer.com
springerlink.com参考文章(28)
J. GALINDO, J. W. GRAHAME, R. K. BUTLIN, An EST-based genome scan using 454 sequencing in the marine snail Littorina saxatilis. Journal of Evolutionary Biology. ,vol. 23, pp. 2004- 2016 ,(2010) , 10.1111/J.1420-9101.2010.02071.X
Paul A. Hohenlohe, Susan Bassham, Paul D. Etter, Nicholas Stiffler, Eric A. Johnson, William A. Cresko, Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags PLoS Genetics. ,vol. 6, pp. e1000862- ,(2010) , 10.1371/JOURNAL.PGEN.1000862
Sarah B. Ng, Emily H. Turner, Peggy D. Robertson, Steven D. Flygare, Abigail W. Bigham, Choli Lee, Tristan Shaffer, Michelle Wong, Arindam Bhattacharjee, Evan E. Eichler, Michael Bamshad, Deborah A. Nickerson, Jay Shendure, Targeted capture and massively parallel sequencing of 12 human exomes Nature. ,vol. 461, pp. 272- 276 ,(2009) , 10.1038/NATURE08250
Christopher W. Wheat, Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing. Genetica. ,vol. 138, pp. 433- 451 ,(2010) , 10.1007/S10709-008-9326-Y
J. CRISTOBAL VERA, CHRISTOPHER W. WHEAT, HOWARD W. FESCEMYER, MIKKO J. FRILANDER, DOUGLAS L. CRAWFORD, ILKKA HANSKI, JAMES H. MARDEN, Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Molecular Ecology. ,vol. 17, pp. 1636- 1647 ,(2008) , 10.1111/J.1365-294X.2008.03666.X
David L Hyten, Qijian Song, Edward W Fickus, Charles V Quigley, Jong-Sung Lim, Ik-Young Choi, Eun-Young Hwang, Marcial Pastor-Corrales, Perry B Cregan, High-throughput SNP discovery and assay development in common bean BMC Genomics. ,vol. 11, pp. 475- 475 ,(2010) , 10.1186/1471-2164-11-475
Ben Langmead, Michael C Schatz, Jimmy Lin, Mihai Pop, Steven L Salzberg, Searching for SNPs with cloud computing Genome Biology. ,vol. 10, pp. 1- 10 ,(2009) , 10.1186/GB-2009-10-11-R134
M F Bonaldo, G Lennon, M B Soares, Normalization and subtraction: two approaches to facilitate gene discovery. Genome Research. ,vol. 6, pp. 791- 806 ,(1996) , 10.1101/GR.6.9.791
Wiesław Babik, Michał Stuglik, Weihong Qi, Marzanna Kuenzli, Katarzyna Kuduk, Paweł Koteja, Jacek Radwan, Heart transcriptome of the bank vole (Myodes glareolus): towards understanding the evolutionary variation in metabolic rate BMC Genomics. ,vol. 11, pp. 390- 390 ,(2010) , 10.1186/1471-2164-11-390
RICHARD J. A. BUGGS, SRIKAR CHAMALA, WEI WU, LU GAO, GREGORY D. MAY, PATRICK S. SCHNABLE, DOUGLAS E. SOLTIS, PAMELA S. SOLTIS, W. BRAD BARBAZUK, Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping. Molecular Ecology. ,vol. 19, pp. 132- 146 ,(2010) , 10.1111/J.1365-294X.2009.04469.X