Next-Generation Sequencing: Principle and Applications to Crops

[1]  Meng Zhang,et al.  The next-generation sequencing technology: A technology review and future perspective , 2010, Science China Life Sciences.

[2]  E. Mardis.  Next-generation DNA sequencing methods. , 2008, Annual review of genomics and human genetics.

[3]  Jan Berka,et al.  A massively parallel PicoTiterPlate™ based platform for discrete picoliter‐scale polymerase chain reactions , 2003, Electrophoresis.

[4]  Gabor T. Marth,et al.  Whole-genome sequencing and variant discovery in C. elegans , 2008, Nature Methods.

[5]  Arthur W. Miller,et al.  DNA sequencing by capillary electrophoresis with replaceable linear polyacrylamide and laser-induced fluorescence detection. , 1993, Analytical chemistry.

[6]  M. Marra,et al.  Applications of next-generation sequencing technologies in functional genomics. , 2008, Genomics.

[7]  M. Metzker.  Sequencing in real time , 2009, Nature Biotechnology.

[8]  D. Spooner,et al.  All biological disciplines that depend on DNA sequence data have been fundamentally changed in the last few years, driven by the development and emergence of next-generation sequenc- , 2012 .

[9]  S. Turner,et al.  Real-Time DNA Sequencing from Single Polymerase Molecules , 2009, Science.

[10]  C. Heiner,et al.  New energy transfer dyes for DNA sequencing. , 1997, Nucleic acids research.

[11]  Timothy B. Stockwell,et al.  Evaluation of next generation sequencing platforms for population targeted sequencing studies , 2009, Genome Biology.

[12]  J. M. Prober,et al.  A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. , 1987, Science.

[13]  F. Sanger,et al.  A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. , 1975, Journal of molecular biology.

[14]  P. Gupta.  Single-molecule DNA sequencing technologies for future genomics research. , 2008, Trends in biotechnology.

[15]  T. Glenn.  Field guide to next‐generation DNA sequencers , 2011, Molecular ecology resources.

[16]  F. Sanger,et al.  DNA sequencing with chain-terminating inhibitors. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[17]  Hanlee P. Ji,et al.  Next-generation DNA sequencing , 2008, Nature Biotechnology.

[18]  Timothy B. Stockwell,et al.  The Sequence of the Human Genome , 2001, Science.

[19]  U Landegren,et al.  A ligase-mediated gene detection technique. , 1988, Science.

[20]  Jonas Korlach,et al.  Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures , 2008, Proceedings of the National Academy of Sciences.

[21]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[22]  S. Deschamps,et al.  Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery , 2010, Molecular Breeding.

[23]  C. Richardson,et al.  Effect of manganese ions on the incorporation of dideoxynucleotides by bacteriophage T7 DNA polymerase and Escherichia coli DNA polymerase I. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Takashi Anazawa,et al.  Multiple Sheath-Flow Gel Capillary-Array Electrophoresis for Multicolor Fluorescent DNA Detection , 1994 .

[25]  Tyson A. Clark,et al.  Direct detection of DNA methylation during single-molecule, real-time sequencing , 2010, Nature Methods.

[26]  A. Tomkinson,et al.  DNA ligases: structure, reaction mechanism, and function. , 2006, Chemical reviews.

[27]  P. Mitra,et al.  Alta-Cyclic: a self-optimizing base caller for next-generation sequencing , 2008, Nature Methods.

[28]  S. Clark,et al.  DNA sequencing using a four‐color confocal fluorescence capillary array scanner , 1996, Electrophoresis.

[29]  Johnf . Thompson,et al.  Virtual Terminator nucleotides for next generation DNA sequencing , 2009, Nature Methods.

[30]  Juliane C. Dohm,et al.  Substantial biases in ultra-short read data sets from high-throughput DNA sequencing , 2008, Nucleic acids research.

[31]  Routine DNA sequencing of 1000 bases in less than one hour by capillary electrophoresis with replaceable linear polyacrylamide solutions. , 1998, Analytical chemistry.

[32]  J. Berka,et al.  Rapid DNA sequencing of more than 1000 bases per run by capillary electrophoresis using replaceable linear polyacrylamide solutions. , 1996, Analytical chemistry.

[33]  J. Shendure,et al.  Materials and Methods Som Text Figs. S1 and S2 Tables S1 to S4 References Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome , 2022 .

[34]  Timothy B. Stockwell,et al.  The Diploid Genome Sequence of an Individual Human , 2007, PLoS biology.

[35]  M. Fedurco,et al.  BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies , 2006, Nucleic acids research.

[36]  W. Gilbert,et al.  A new method for sequencing DNA. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[37]  M. Metzker,et al.  Electrophoretically Uniform Fluorescent Dyes for Automated DNA Sequencing , 1996, Science.

[38]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[39]  Nancy F. Hansen,et al.  Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry , 2008, Nature.

[40]  E. Mardis.  The impact of next-generation sequencing technology on genetics. , 2008, Trends in genetics : TIG.

[41]  A. Tretyn,et al.  Sequencing technologies and genome sequencing , 2011, Journal of Applied Genetics.

[42]  R. Chiodini,et al.  The impact of next-generation sequencing on genomics. , 2011, Journal of genetics and genomics = Yi chuan xue bao.

[43]  D. Bentley,et al.  Whole-genome re-sequencing. , 2006, Current opinion in genetics & development.

[44]  S. Quake,et al.  Single-Molecule DNA Sequencing of a Viral Genome , 2008, Science.

[45]  Jingyue Ju,et al.  Four-color DNA sequencing with 3′-O-modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides , 2008, Proceedings of the National Academy of Sciences.

[46]  Lloyd M. Smith,et al.  Fluorescence detection in automated DNA sequence analysis , 1986, Nature.

[47]  D. Dressman,et al.  Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[48]  M. Ronaghi,et al.  A Sequencing Method Based on Real-Time Pyrophosphate , 1998, Science.

[49]  J. Bähler,et al.  Next-generation sequencing: applications beyond genomes , 2008, Biochemical Society transactions.

[50]  R A Mathies,et al.  Fluorescence energy transfer dye-labeled primers for DNA sequencing and analysis. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[51]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.