Microsatellite marker discovery using single molecule real-time circular consensus sequencing on the Pacific Biosciences RS.
作者： Markus A. Grohme , Roberto Frias Soler , Michael Wink , Marcus Frohme
DOI: 10.2144/000114104
关键词: Shotgun sequencing 、 Marker Discovery 、 Genetics 、 Population genetics 、 Computational biology 、 Consensus sequence 、 Microsatellite 、 Genome 、 Biology 、 Primer (molecular biology) 、 Pacific biosciences
摘要: Microsatellite sequences are important markers for population genetics studies. In the past, development of adequate microsatellite primers has been cumbersome. However with advent next-generation sequencing technologies, marker identification in genomes non-model species greatly simplified. Here we describe discovery on a Pacific Biosciences single molecule real-time sequencer. For Greater White-fronted Goose (Anser albifrons), identified 316 loci genome shotgun experiment. We found that capability handling large insert sizes and high quality circular consensus provides an advantage over short read technologies primer design. Combined straightforward amplification-free library preparation, PacBio is economically viable alternative subsequent PCR
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sci-hub.se 参考文章(19)
Thibaut Malausa, André Gilles, Emese Meglécz, Hélène Blanquart, Stéphanie Duthoy, Caroline Costedoat, Vincent Dubut, Nicolas Pech, PHILIPPE CASTAGNONE‐SERENO, Christophe Delye, Nicolas Feau, Pascal Frey, Philippe Gauthier, Thomas Guillemaud, Laurent Hazard, Valérie Le Corre, BRIGITTE LUNG‐ESCARMANT, Pierre‐Jean G Malé, Stéphanie Ferreira, Jean‐François Martin, None, High-throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries Molecular Ecology Resources. ,vol. 11, pp. 638- 644 ,(2011) , 10.1111/J.1755-0998.2011.02992.X
Emese Meglecz, Gabriel Neve, Ed Biffin, Michael G Gardner, None, Breakdown of Phylogenetic Signal: A Survey of Microsatellite Densities in 454 Shotgun Sequences from 154 Non Model Eukaryote Species PLoS ONE. ,vol. 7, pp. e40861- ,(2012) , 10.1371/JOURNAL.PONE.0040861
André Gilles, Emese Meglécz, Nicolas Pech, Stéphanie Ferreira, Thibaut Malausa, Jean-François Martin, None, Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing BMC Genomics. ,vol. 12, pp. 245- 245 ,(2011) , 10.1186/1471-2164-12-245
Quentin C. Santana, Martin P. A. Coetzee, Emma T. Steenkamp, Osmond X. Mlonyeni, Gifty N. A. Hammond, Michael J. Wingfield, Brenda D. Wingfield, Microsatellite discovery by deep sequencing of enriched genomic libraries. BioTechniques. ,vol. 46, pp. 217- 223 ,(2009) , 10.2144/000113085
Francois Rousset, None, genepop'007: a complete re-implementation of the genepop software for Windows and Linux Molecular Ecology Resources. ,vol. 8, pp. 103- 106 ,(2008) , 10.1111/J.1471-8286.2007.01931.X
Todd A. Castoe, Alexander W. Poole, A. P. Jason de Koning, Kenneth L. Jones, Diana F. Tomback, Sara J. Oyler-McCance, Jennifer A. Fike, Stacey L. Lance, Jeffrey W. Streicher, Eric N. Smith, David D. Pollock, Rapid Microsatellite Identification from Illumina Paired-End Genomic Sequencing in Two Birds and a Snake PLoS ONE. ,vol. 7, pp. e30953- ,(2012) , 10.1371/JOURNAL.PONE.0030953
Kensuke Nakamura, Taku Oshima, Takuya Morimoto, Shun Ikeda, Hirofumi Yoshikawa, Yuh Shiwa, Shu Ishikawa, Margaret C. Linak, Aki Hirai, Hiroki Takahashi, Md. Altaf-Ul-Amin, Naotake Ogasawara, Shigehiko Kanaya, Sequence-specific error profile of Illumina sequencers Nucleic Acids Research. ,vol. 39, ,(2011) , 10.1093/NAR/GKR344
H. Li, R. Durbin, Fast and accurate short read alignment with Burrows–Wheeler transform Bioinformatics. ,vol. 25, pp. 1754- 1760 ,(2009) , 10.1093/BIOINFORMATICS/BTP324
Craig R. Primmer, Terje Raudsepp, Bhanu P. Chowdhary, Anders Pape Møller, Hans Ellegren, Low Frequency of Microsatellites in the Avian Genome Genome Research. ,vol. 7, pp. 471- 482 ,(1997) , 10.1101/GR.7.5.471
T. N. JENNINGS, B. J. KNAUS, T. D. MULLINS, S. M. HAIG, R. C. CRONN, Multiplexed microsatellite recovery using massively parallel sequencing. Molecular Ecology Resources. ,vol. 11, pp. 1060- 1067 ,(2011) , 10.1111/J.1755-0998.2011.03033.X