What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research

Bräutigam A, Gowik U (2010)
Plant Biology 12(6): 831-841.

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Next generation sequencing (NGS) technologies have opened fascinating opportunities for the analysis of plants with and without a sequenced genome on a genomic scale. During the last few years, NGS methods have become widely available and cost effective. They can be applied to a wide variety of biological questions, from the sequencing of complete eukaryotic genomes and transcriptomes, to the genome-scale analysis of DNA-protein interactions. In this review, we focus on the use of NGS for plant transcriptomics, including gene discovery, transcript quantification and marker discovery for non-model plants, as well as transcript annotation and quantification, small RNA discovery and antisense transcription analysis for model plants. We discuss the experimental design for analysis of plants with and without a sequenced genome, including considerations on sampling, RNA preparation, sequencing platforms and bioinformatics tools for data analysis. NGS technologies offer exciting new opportunities for the plant sciences, especially for work on plants without a sequenced genome, since large sequence resources can be generated at moderate cost.
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Plant Biology
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12
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6
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831-841
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Bräutigam A, Gowik U. What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research. Plant Biology. 2010;12(6):831-841.
Bräutigam, A., & Gowik, U. (2010). What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research. Plant Biology, 12(6), 831-841. doi:10.1111/j.1438-8677.2010.00373.x
Bräutigam, A., and Gowik, U. (2010). What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research. Plant Biology 12, 831-841.
Bräutigam, A., & Gowik, U., 2010. What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research. Plant Biology, 12(6), p 831-841.
A. Bräutigam and U. Gowik, “What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research”, Plant Biology, vol. 12, 2010, pp. 831-841.
Bräutigam, A., Gowik, U.: What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research. Plant Biology. 12, 831-841 (2010).
Bräutigam, Andrea, and Gowik, Udo. “What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research”. Plant Biology 12.6 (2010): 831-841.
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61 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

New perspectives on the evolution of plant mating systems.
Karron JD, Ivey CT, Mitchell RJ, Whitehead MR, Peakall R, Case AL., Ann Bot 109(3), 2012
PMID: 22210849
An mRNA blueprint for C4 photosynthesis derived from comparative transcriptomics of closely related C3 and C4 species.
Bräutigam A, Kajala K, Wullenweber J, Sommer M, Gagneul D, Weber KL, Carr KM, Gowik U, Mass J, Lercher MJ, Westhoff P, Hibberd JM, Weber AP., Plant Physiol 155(1), 2011
PMID: 20543093
First off the mark: early seed germination.
Weitbrecht K, Müller K, Leubner-Metzger G., J Exp Bot 62(10), 2011
PMID: 21430292
Exploiting the engine of C(4) photosynthesis.
Sage RF, Zhu XG., J Exp Bot 62(9), 2011
PMID: 21652533
New approaches to Prunus transcriptome analysis.
Martínez-Gómez P, Crisosto CH, Bonghi C, Rubio M., Genetica 139(6), 2011
PMID: 21584650
Field guide to next-generation DNA sequencers.
Glenn TC., Mol Ecol Resour 11(5), 2011
PMID: 21592312
Transcriptome profiling and insilico analysis of Gynostemma pentaphyllum using a next generation sequencer.
Subramaniyam S, Mathiyalagan R, Jun Gyo I, Bum-Soo L, Sungyoung L, Deok Chun Y., Plant Cell Rep 30(11), 2011
PMID: 21769605
Transcriptomic resilience to global warming in the seagrass Zostera marina, a marine foundation species.
Franssen SU, Gu J, Bergmann N, Winters G, Klostermeier UC, Rosenstiel P, Bornberg-Bauer E, Reusch TB., Proc Natl Acad Sci U S A 108(48), 2011
PMID: 22084086

85 References

Daten bereitgestellt von Europe PubMed Central.

A gene expression signature shared by human mature oocytes and embryonic stem cells.
Assou S, Cerecedo D, Tondeur S, Pantesco V, Hovatta O, Klein B, Hamamah S, De Vos J., BMC Genomics 10(), 2009
PMID: 19128516
Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing.
Weber AP, Weber KL, Carr K, Wilkerson C, Ohlrogge JB., Plant Physiol. 144(1), 2007
PMID: 17351049
The 1001 genomes project for Arabidopsis thaliana.
Weigel D, Mott R., Genome Biol. 10(5), 2009
PMID: 19519932
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution.
Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J, Bahler J., Nature 453(7199), 2008
PMID: 18488015
The isolation of nuclei from tissue-cultured plant cells.
Willmitzer L, Wagner KG., Exp. Cell Res. 135(1), 1981
PMID: 6269864
Cloning and characterization of microRNAs from wheat (Triticum aestivum L.).
Yao Y, Guo G, Ni Z, Sunkar R, Du J, Zhu JK, Sun Q., Genome Biol. 8(6), 2007
PMID: 17543110
Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.).
Zhao CZ, Xia H, Frazier TP, Yao YY, Bi YP, Li AQ, Li MJ, Li CS, Zhang BH, Wang XJ., BMC Plant Biol. 10(), 2010
PMID: 20047695
A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains.
Zhu QH, Spriggs A, Matthew L, Fan L, Kennedy G, Gubler F, Helliwell C., Genome Res. 18(9), 2008
PMID: 18687877

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