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.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
OA 274.73 KB
Autor*in
Abstract / Bemerkung
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.
Stichworte
Application; non-model species; protocol; RNA-seq; transcriptomics
Erscheinungsjahr
2010
Zeitschriftentitel
Plant Biology
Band
12
Ausgabe
6
Seite(n)
831-841
ISSN
1435-8603
eISSN
1438-8677
Page URI
https://pub.uni-bielefeld.de/record/2915165

Zitieren

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.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Copyright Statement:
This Item is protected by copyright and/or related rights. [...]
Volltext(e)
Access Level
OA Open Access
Zuletzt Hochgeladen
2019-09-06T09:18:54Z
MD5 Prüfsumme
8b11738b93a27806ae56aa9acf238b0c

66 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Usability of reference-free transcriptome assemblies for detection of differential expression: a case study on Aethionema arabicum dimorphic seeds.
Wilhelmsson PKI, Chandler JO, Fernandez-Pozo N, Graeber K, Ullrich KK, Arshad W, Khan S, Hofberger JA, Buchta K, Edger PP, Pires JC, Schranz ME, Leubner-Metzger G, Rensing SA., BMC Genomics 20(1), 2019
PMID: 30700268
The use of chloroplast genome sequences to solve phylogenetic incongruences in Polystachya Hook (Orchidaceae Juss).
de Abreu NL, Alves RJV, Cardoso SRS, Bertrand YJK, Sousa F, Hall CF, Pfeil BE, Antonelli A., PeerJ 6(), 2018
PMID: 29922511
Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos.
Rodrigues AS, De Vega JJ, Miguel CM., BMC Plant Biol 18(1), 2018
PMID: 30594130
Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants: The Omics Strategies.
Meena KK, Sorty AM, Bitla UM, Choudhary K, Gupta P, Pareek A, Singh DP, Prabha R, Sahu PK, Gupta VK, Singh HB, Krishanani KK, Minhas PS., Front Plant Sci 8(), 2017
PMID: 28232845
Exploring the heat-responsive chaperones and microsatellite markers associated with terminal heat stress tolerance in developing wheat.
Kumar RR, Goswami S, Shamim M, Dubey K, Singh K, Singh S, Kala YK, Niraj RRK, Sakhrey A, Singh GP, Grover M, Singh B, Rai GK, Rai AK, Chinnusamy V, Praveen S., Funct Integr Genomics 17(6), 2017
PMID: 28573536
OMICS Technologies and Applications in Sugar Beet.
Zhang Y, Nan J, Yu B., Front Plant Sci 7(), 2016
PMID: 27446130
Efficient and Heritable Targeted Mutagenesis in Mosses Using the CRISPR/Cas9 System.
Nomura T, Sakurai T, Osakabe Y, Osakabe K, Sakakibara H., Plant Cell Physiol 57(12), 2016
PMID: 27986915
First report of resistance to acetolactate-synthase-inhibiting herbicides in yellow nutsedge (Cyperus esculentus): confirmation and characterization.
Tehranchian P, Norsworthy JK, Nandula V, McElroy S, Chen S, Scott RC., Pest Manag Sci 71(9), 2015
PMID: 25307777
Comparative whole-genome analyses of selection marker-free rice-based cholera toxin B-subunit vaccine lines and wild-type lines.
Kashima K, Mejima M, Kurokawa S, Kuroda M, Kiyono H, Yuki Y., BMC Genomics 16(), 2015
PMID: 25653106
RNA sequencing of Populus x canadensis roots identifies key molecular mechanisms underlying physiological adaption to excess zinc.
Ariani A, Di Baccio D, Romeo S, Lombardi L, Andreucci A, Lux A, Horner DS, Sebastiani L., PLoS One 10(2), 2015
PMID: 25671786
Ion Torrent sequencing as a tool for mutation discovery in the flax (Linum usitatissimum L.) genome.
Galindo-González L, Pinzón-Latorre D, Bergen EA, Jensen DC, Deyholos MK., Plant Methods 11(), 2015
PMID: 25788971
MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes.
Chamala S, García N, Godden GT, Krishnakumar V, Jordon-Thaden IE, De Smet R, Barbazuk WB, Soltis DE, Soltis PS., Appl Plant Sci 3(4), 2015
PMID: 25909041
RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications.
Lyu MJ, Gowik U, Kelly S, Covshoff S, Mallmann J, Westhoff P, Hibberd JM, Stata M, Sage RF, Lu H, Wei X, Wong GK, Zhu XG., BMC Evol Biol 15(), 2015
PMID: 26084484
Towards a better monitoring of seed ageing under ex situ seed conservation.
Fu YB, Ahmed Z, Diederichsen A., Conserv Physiol 3(1), 2015
PMID: 27293711
A genome-scale mining strategy for recovering novel rapidly-evolving nuclear single-copy genes for addressing shallow-scale phylogenetics in Hydrangea.
Granados Mendoza C, Naumann J, Samain MS, Goetghebeur P, De Smet Y, Wanke S., BMC Evol Biol 15(), 2015
PMID: 26141718
Plot size matters: interference from intergenotypic competition in plant phenotyping studies
Rebetzke GJ, Fischer R(A, van Herwaarden AF, Bonnett DG, Chenu K, Rattey AR, Fettell NA., Funct Plant Biol 41(2), 2014
PMID: IND500717050
Azolla domestication towards a biobased economy?
Brouwer P, Bräutigam A, Külahoglu C, Tazelaar AO, Kurz S, Nierop KG, van der Werf A, Weber AP, Schluepmann H., New Phytol 202(3), 2014
PMID: 24494738
Comparative studies of C3 and C4 Atriplex hybrids in the genomics era: physiological assessments.
Oakley JC, Sultmanis S, Stinson CR, Sage TL, Sage RF., J Exp Bot 65(13), 2014
PMID: 24675672
Future of portable devices for plant pathogen diagnosis.
Nezhad AS., Lab Chip 14(16), 2014
PMID: 24920461
Transcriptome characterization and differential expression analysis of cold-responsive genes in young spikes of common wheat.
Zhang S, Song G, Gao J, Li Y, Guo D, Fan Q, Sui X, Chu X, Huang C, Liu J, Li G., J Biotechnol 189(), 2014
PMID: 25240441
Transcriptomic profiling of the salt-stress response in the wild recretohalophyte Reaumuria trigyna.
Dang ZH, Zheng LL, Wang J, Gao Z, Wu SB, Qi Z, Wang YC., BMC Genomics 14(), 2013
PMID: 23324106
Metabolic engineering with plants for a sustainable biobased economy.
Yoon JM, Zhao L, Shanks JV., Annu Rev Chem Biomol Eng 4(), 2013
PMID: 23540288
Biogenesis, evolution, and functions of plant microRNAs.
Pashkovskiy PP, Ryazansky SS., Biochemistry (Mosc) 78(6), 2013
PMID: 23980889
The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability.
Li JW, Bolser D, Manske M, Giorgi FM, Vyahhi N, Usadel B, Clavijo BJ, Chan TF, Wong N, Zerbino D, Schneider MV., Brief Bioinform 14(5), 2013
PMID: 23793381
Integrated transcriptomics and metabolomics decipher differences in the resistance of pedunculate oak to the herbivore Tortrix viridana L.
Kersten B, Ghirardo A, Schnitzler JP, Kanawati B, Schmitt-Kopplin P, Fladung M, Schroeder H., BMC Genomics 14(), 2013
PMID: 24160444
Quantitative and qualitative differences in celiac disease epitopes among durum wheat varieties identified through deep RNA-amplicon sequencing.
Salentijn EM, Esselink DG, Goryunova SV, van der Meer IM, Gilissen LJ, Smulders MJ., BMC Genomics 14(), 2013
PMID: 24354426
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
Eco-evolutionary dynamics in a changing world.
Hanski I., Ann N Y Acad Sci 1249(), 2012
PMID: 22335524
Genetic and genomic approaches for R-gene mediated disease resistance in tomato: retrospects and prospects.
Ercolano MR, Sanseverino W, Carli P, Ferriello F, Frusciante L., Plant Cell Rep 31(6), 2012
PMID: 22350316
Application of genomic tools in plant breeding.
Pérez-de-Castro AM, Vilanova S, Cañizares J, Pascual L, Blanca JM, Díez MJ, Prohens J, Picó B., Curr Genomics 13(3), 2012
PMID: 23115520
Using nuclear gene data for plant phylogenetics: progress and prospects.
Zimmer EA, Wen J., Mol Phylogenet Evol 65(2), 2012
PMID: 22842093
Large-scale transcriptome characterization and mass discovery of SNPs in globe artichoke and its related taxa.
Scaglione D, Lanteri S, Acquadro A, Lai Z, Knapp SJ, Rieseberg L, Portis E., Plant Biotechnol J 10(8), 2012
PMID: 22849342
Are we ready for genome-scale modeling in plants?
Collakova E, Yen JY, Senger RS., Plant Sci 191-(), 2012
PMID: IND44785982
The bench scientist's guide to statistical analysis of RNA-Seq data.
Yendrek CR, Ainsworth EA, Thimmapuram J., BMC Res Notes 5(), 2012
PMID: 22980220
Why assembling plant genome sequences is so challenging.
Claros MG, Bautista R, Guerrero-Fernández D, Benzerki H, Seoane P, Fernández-Pozo N., Biology (Basel) 1(2), 2012
PMID: 24832233
Transcriptome-scale homoeolog-specific transcript assemblies of bread wheat.
Schreiber AW, Hayden MJ, Forrest KL, Kong SL, Langridge P, Baumann U., BMC Genomics 13(), 2012
PMID: 22989011
Application of large-scale sequencing to marker discovery in plants.
Henry RJ, Edwards M, Waters DL, Gopala Krishnan S, Bundock P, Sexton TR, Masouleh AK, Nock CJ, Pattemore J., J Biosci 37(5), 2012
PMID: 23107919
Next generation sequencing and de novo transcriptome analysis of Costus pictus D. Don, a non-model plant with potent anti-diabetic properties.
Annadurai RS, Jayakumar V, Mugasimangalam RC, Katta MA, Anand S, Gopinathan S, Sarma SP, Fernandes SJ, Mullapudi N, Murugesan S, Rao SN., BMC Genomics 13(), 2012
PMID: 23176672
MicroRNAs play critical roles during plant development and in response to abiotic stresses.
de Lima JC, Loss-Morais G, Margis R., Genet Mol Biol 35(4 (suppl)), 2012
PMID: 23412556
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
Evolution of C4 photosynthesis in the genus Flaveria: how many and which genes does it take to make C4?
Gowik U, Bräutigam A, Weber KL, Weber AP, Westhoff P., Plant Cell 23(6), 2011
PMID: 21705644
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.

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ., Nucleic Acids Res. 25(17), 1997
PMID: 9254694
High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies.
Aury JM, Cruaud C, Barbe V, Rogier O, Mangenot S, Samson G, Poulain J, Anthouard V, Scarpelli C, Artiguenave F, Wincker P., BMC Genomics 9(), 2008
PMID: 19087275
Large-scale identification of microRNAs from a basal eudicot (Eschscholzia californica) and conservation in flowering plants.
Barakat A, Wall K, Leebens-Mack J, Wang YJ, Carlson JE, Depamphilis CW., Plant J. 51(6), 2007
PMID: 17635767
Expression of genes associated with carbohydrate metabolism in cotton stems and roots.
Taliercio EW, Romano G, Scheffler J, Ayre BG., BMC Plant Biol. 9(), 2009
PMID: 19161628
Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing.
Bundock PC, Eliott FG, Ablett G, Benson AD, Casu RE, Aitken KS, Henry RJ., Plant Biotechnol. J. 7(4), 2009
PMID: 19386042
Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology.
Cheung F, Haas BJ, Goldberg SM, May GD, Xiao Y, Town CD., BMC Genomics 7(), 2006
PMID: 17062153
Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs.
Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Muller WE, Wetter T, Suhai S., Genome Res. 14(6), 2004
PMID: 15140833
Stem cell transcriptome profiling via massive-scale mRNA sequencing.
Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G, Robertson AJ, Perkins AC, Bruce SJ, Lee CC, Ranade SS, Peckham HE, Manning JM, McKernan KJ, Grimmond SM., Nat. Methods 5(7), 2008
PMID: 18516046
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.
Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE., Nature 452(7184), 2008
PMID: 18278030
Shedding light on an extremophile lifestyle through transcriptomics.
Dassanayake M, Haas JS, Bohnert HJ, Cheeseman JM., New Phytol. 183(3), 2009
PMID: 19549131
Conifers have a unique small RNA silencing signature
Dolgosheina, RNA-A Publication of the RNA Society 14(), 2008
Real-time DNA sequencing from single polymerase molecules.
Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S, Dalal R, Dewinter A, Dixon J, Foquet M, Gaertner A, Hardenbol P, Heiner C, Hester K, Holden D, Kearns G, Kong X, Kuse R, Lacroix Y, Lin S, Lundquist P, Ma C, Marks P, Maxham M, Murphy D, Park I, Pham T, Phillips M, Roy J, Sebra R, Shen G, Sorenson J, Tomaney A, Travers K, Trulson M, Vieceli J, Wegener J, Wu D, Yang A, Zaccarin D, Zhao P, Zhong F, Korlach J, Turner S., Science 323(5910), 2008
PMID: 19023044
Gene discovery and annotation using LCM-454 transcriptome sequencing.
Emrich SJ, Barbazuk WB, Li L, Schnable PS., Genome Res. 17(1), 2006
PMID: 17095711
Sense from sequence reads: methods for alignment and assembly.
Flicek P, Birney E., Nat. Methods 6(11 Suppl), 2009
PMID: 19844229
The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access.
Goda H, Sasaki E, Akiyama K, Maruyama-Nakashita A, Nakabayashi K, Li W, Ogawa M, Yamauchi Y, Preston J, Aoki K, Kiba T, Takatsuto S, Fujioka S, Asami T, Nakano T, Kato H, Mizuno T, Sakakibara H, Yamaguchi S, Nambara E, Kamiya Y, Takahashi H, Hirai MY, Sakurai T, Shinozaki K, Saito K, Yoshida S, Shimada Y., Plant J. 55(3), 2008
PMID: 18419781
Consed: a graphical tool for sequence finishing.
Gordon D, Abajian C, Green P., Genome Res. 8(3), 1998
PMID: 9521923
Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning.
Henderson IR, Zhang X, Lu C, Johnson L, Meyers BC, Green PJ, Jacobsen SE., Nat. Genet. 38(6), 2006
PMID: 16699516
The new paradigm of flow cell sequencing.
Holt RA, Jones SJ., Genome Res. 18(6), 2008
PMID: 18519653
CAP3: A DNA sequence assembly program.
Huang X, Madan A., Genome Res. 9(9), 1999
PMID: 10508846
Discovering genetic polymorphisms in next-generation sequencing data.
Imelfort M, Duran C, Batley J, Edwards D., Plant Biotechnol. J. 7(4), 2009
PMID: 19386039
MicroRNAS and their regulatory roles in plants.
Jones-Rhoades MW, Bartel DP, Bartel B., Annu Rev Plant Biol 57(), 2006
PMID: 16669754
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.
Jothi R, Cuddapah S, Barski A, Cui K, Zhao K., Nucleic Acids Res. 36(16), 2008
PMID: 18684996
Antisense transcription in the mammalian transcriptome.
Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, Suzuki H, Carninci P, Hayashizaki Y, Wells C, Frith M, Ravasi T, Pang KC, Hallinan J, Mattick J, Hume DA, Lipovich L, Batalov S, Engstrom PG, Mizuno Y, Faghihi MA, Sandelin A, Chalk AM, Mottagui-Tabar S, Liang Z, Lenhard B, Wahlestedt C; RIKEN Genome Exploration Research Group; Genome Science Group (Genome Network Project Core Group); FANTOM Consortium., Science 309(5740), 2005
PMID: 16141073
BLAT--the BLAST-like alignment tool.
Kent WJ., Genome Res. 12(4), 2002
PMID: 11932250
The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses.
Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, D'Angelo C, Bornberg-Bauer E, Kudla J, Harter K., Plant J. 50(2), 2007
PMID: 17376166
Identification of a spontaneous frame shift mutation in a non-reference Arabidopsis thaliana accession using whole genome sequencing
Laitinen, Plant Physiology (), 2010
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead B, Trapnell C, Pop M, Salzberg SL., Genome Biol. 10(3), 2009
PMID: 19261174
Sampling the Waterhemp (Amaranthus tuberculatus) Genome Using Pyrosequencing Technology
Lee RyanM, Thimmapuram Jyothi, Thinglum KateA, Gong George, Hernandez AlvaroG, Wright ChrisL, Kim RyanW, Mikel MarkA, Tranel PatrickJ., Weed Sci. 57(5), 2009
PMID: IND44263840
SOAP: short oligonucleotide alignment program.
Li R, Li Y, Kristiansen K, Wang J., Bioinformatics 24(5), 2008
PMID: 18227114
SOAP2: an improved ultrafast tool for short read alignment.
Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J., Bioinformatics 25(15), 2009
PMID: 19497933
The sequence and de novo assembly of the giant panda genome.
Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W, Li J, Wei F, Li H, Jian M, Li J, Zhang Z, Nielsen R, Li D, Gu W, Yang Z, Xuan Z, Ryder OA, Leung FC, Zhou Y, Cao J, Sun X, Fu Y, Fang X, Guo X, Wang B, Hou R, Shen F, Mu B, Ni P, Lin R, Qian W, Wang G, Yu C, Nie W, Wang J, Wu Z, Liang H, Min J, Wu Q, Cheng S, Ruan J, Wang M, Shi Z, Wen M, Liu B, Ren X, Zheng H, Dong D, Cook K, Shan G, Zhang H, Kosiol C, Xie X, Lu Z, Zheng H, Li Y, Steiner CC, Lam TT, Lin S, Zhang Q, Li G, Tian J, Gong T, Liu H, Zhang D, Fang L, Ye C, Zhang J, Hu W, Xu A, Ren Y, Zhang G, Bruford MW, Li Q, Ma L, Guo Y, An N, Hu Y, Zheng Y, Shi Y, Li Z, Liu Q, Chen Y, Zhao J, Qu N, Zhao S, Tian F, Wang X, Wang H, Xu L, Liu X, Vinar T, Wang Y, Lam TW, Yiu SM, Liu S, Zhang H, Li D, Huang Y, Wang X, Yang G, Jiang Z, Wang J, Qin N, Li L, Li J, Bolund L, Kristiansen K, Wong GK, Olson M, Zhang X, Li S, Yang H, Wang J, Wang J., Nature 463(7279), 2009
PMID: 20010809
ZOOM! Zillions of oligos mapped.
Lin H, Zhang Z, Zhang MQ, Ma B, Li M., Bioinformatics 24(21), 2008
PMID: 18684737
Highly integrated single-base resolution maps of the epigenome in Arabidopsis.
Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR., Cell 133(3), 2008
PMID: 18423832
Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond.
Lister R, Gregory BD, Ecker JR., Curr. Opin. Plant Biol. 12(2), 2009
PMID: 19157957
MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant.
Lu C, Kulkarni K, Souret FF, MuthuValliappan R, Tej SS, Poethig RS, Henderson IR, Jacobsen SE, Wang W, Green PJ, Meyers BC., Genome Res. 16(10), 2006
PMID: 16954541
Next-generation DNA sequencing methods.
Mardis ER., Annu Rev Genomics Hum Genet 9(), 2008
PMID: 18576944
Gene expression analysis of plant host-pathogen interactions by SuperSAGE
Matsumura, Proceedings of the National Academy of Sciences USA 100(), 2003
SuperSAGE: a modern platform for genome-wide quantitative transcript profiling.
Matsumura H, Kruger DH, Kahl G, Terauchi R., Curr Pharm Biotechnol 9(5), 2008
PMID: 18855689
Sequencing technologies - the next generation.
Metzker ML., Nat. Rev. Genet. 11(1), 2009
PMID: 19997069
The use of MPSS for whole-genome transcriptional analysis in Arabidopsis.
Meyers BC, Tej SS, Vu TH, Haudenschild CD, Agrawal V, Edberg SB, Ghazal H, Decola S., Genome Res. 14(8), 2004
PMID: 15289482
SuperSAGE: the drought stress-responsive transcriptome of chickpea roots.
Molina C, Rotter B, Horres R, Udupa SM, Besser B, Bellarmino L, Baum M, Matsumura H, Terauchi R, Kahl G, Winter P., BMC Genomics 9(), 2008
PMID: 19025623
Metabolic engineering of potato tuber carotenoids through tuber-specific silencing of lycopene epsilon cyclase.
Diretto G, Tavazza R, Welsch R, Pizzichini D, Mourgues F, Papacchioli V, Beyer P, Giuliano G., BMC Plant Biol. 6(), 2006
PMID: 16800876
Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa.
Morin RD, Aksay G, Dolgosheina E, Ebhardt HA, Magrini V, Mardis ER, Sahinalp SC, Unrau PJ., Genome Res. 18(4), 2008
PMID: 18323537
Mapping and quantifying mammalian transcriptomes by RNA-Seq.
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B., Nat. Methods 5(7), 2008
PMID: 18516045
The transcriptional landscape of the yeast genome defined by RNA sequencing.
Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M., Science 320(5881), 2008
PMID: 18451266
SSAHA: a fast search method for large DNA databases.
Ning Z, Cox AJ, Mullikin JC., Genome Res. 11(10), 2001
PMID: 11591649
Distinct size distribution of endogeneous siRNAs in maize: evidence from deep sequencing in the mop1-1 mutant
Nobuta, Proceedings of the National Academy of Sciences USA 105(), 2008
Virulence factor rtx in Legionella pneumophila, evidence suggesting it is a modular multifunctional protein.
D'Auria G, Jimenez N, Peris-Bondia F, Pelaz C, Latorre A, Moya A., BMC Genomics 9(), 2008
PMID: 18194518
Sequencing of natural strains of Arabidopsis thaliana with short reads.
Ossowski S, Schneeberger K, Clark RM, Lanz C, Warthmann N, Weigel D., Genome Res. 18(12), 2008
PMID: 18818371
Mapping accuracy of short reads from massively parallel sequencing and the implications for quantitative expression profiling
Palmieri, PLoS ONE 4(), 2009
Computation for ChIP-seq and RNA-seq studies.
Pepke S, Wold B, Mortazavi A., Nat. Methods 6(11 Suppl), 2009
PMID: 19844228
Bioinformatics challenges of new sequencing technology.
Pop M, Salzberg SL., Trends Genet. 24(3), 2008
PMID: 18262676
Single-molecule sequencing of an individual human genome.
Pushkarev D, Neff NF, Quake SR., Nat. Biotechnol. 27(9), 2009
PMID: 19668243
A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana
Rajagopalan, Genes and Development 20(), 2006
DNA SEQUENCING: a sequencing method based on real-time pyrophosphate
Ronaghi, Science 281(), 1998

Sambrook, 2001
A gene expression map of Arabidopsis thaliana development.
Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU., Nat. Genet. 37(5), 2005
PMID: 15806101
SHOREmap: simultaneous mapping and mutation identification by deep sequencing.
Schneeberger K, Ossowski S, Lanz C, Juul T, Petersen AH, Nielsen KL, Jorgensen JE, Weigel D, Andersen SU., Nat. Methods 6(8), 2009
PMID: 19644454
Next-generation DNA sequencing.
Shendure J, Ji H., Nat. Biotechnol. 26(10), 2008
PMID: 18846087
Accurate multiplex polony sequencing of an evolved bacterial genome.
Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM., Science 309(5741), 2005
PMID: 16081699
Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags.
Shin H, Hirst M, Bainbridge MN, Magrini V, Mardis E, Moerman DG, Marra MA, Baillie DL, Jones SJ., BMC Biol. 6(), 2008
PMID: 18611272
Short-read sequencing technologies for transcriptional analyses.
Simon SA, Zhai J, Nandety RS, McCormick KP, Zeng J, Mejia D, Meyers BC., Annu Rev Plant Biol 60(), 2009
PMID: 19575585
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome.
Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, Schmidt D, O'Keeffe S, Haas S, Vingron M, Lehrach H, Yaspo ML., Science 321(5891), 2008
PMID: 18599741
Identification of novel and candidate miRNAs in rice by high throughput sequencing.
Sunkar R, Zhou X, Zheng Y, Zhang W, Zhu JK., BMC Plant Biol. 8(), 2008
PMID: 18312648
Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L.) Wilczek).
Tangphatsornruang S, Somta P, Uthaipaisanwong P, Chanprasert J, Sangsrakru D, Seehalak W, Sommanas W, Tragoonrung S, Srinives P., BMC Plant Biol. 9(), 2009
PMID: 19930676
Gene expression profiling by massively parallel sequencing.
Torres TT, Metta M, Ottenwalder B, Schlotterer C., Genome Res. 18(1), 2007
PMID: 18032722
Post-transcriptional small RNA pathways in plants: mechanisms and regulations
Vaucheret, Genes and Development 20(), 2006
Serial analysis of gene expression.
Velculescu VE, Zhang L, Vogelstein B, Kinzler KW., Science 270(5235), 1995
PMID: 7570003
Comparison of next generation sequencing technologies for transcriptome characterization.
Wall PK, Leebens-Mack J, Chanderbali AS, Barakat A, Wolcott E, Liang H, Landherr L, Tomsho LP, Hu Y, Carlson JE, Ma H, Schuster SC, Soltis DE, Soltis PS, Altman N, dePamphilis CW., BMC Genomics 10(), 2009
PMID: 19646272
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

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 21040298
PubMed | Europe PMC

Suchen in

Google Scholar