RNA-seq assembly - are we there yet?

Schliesky S, Gowik U, Weber APM, Bräutigam A (2012)
Frontiers in Plant Science 3: 220.

OA 1.24 MB
Zeitschriftenaufsatz | Veröffentlicht | Englisch
; ; ;
Abstract / Bemerkung
Transcriptomic sequence resources represent invaluable assets for research, in particular for non-model species without a sequenced genome. To date, the Next Generation Sequencing technologies 454/Roche and Illumina have been used to generate transcriptome sequence databases by mRNA-Seq for more than fifty different plant species. While some of the databases were successfully used for downstream applications, such as proteomics, the assembly parameters indicate that the assemblies do not yet accurately reflect the actual plant transcriptomes. Two different assembly strategies have been used, overlap consensus based assemblers for long reads and Eulerian path/de Bruijn graph assembler for short reads. In this review, we discuss the challenges and solutions to the transcriptome assembly problem. A list of quality control parameters and the necessary scripts to produce them are provided.
Frontiers in Plant Science


Schliesky S, Gowik U, Weber APM, Bräutigam A. RNA-seq assembly - are we there yet? Frontiers in Plant Science. 2012;3: 220.
Schliesky, S., Gowik, U., Weber, A. P. M., & Bräutigam, A. (2012). RNA-seq assembly - are we there yet? Frontiers in Plant Science, 3, 220. doi:10.3389/fpls.2012.00220
Schliesky, S., Gowik, U., Weber, A. P. M., and Bräutigam, A. (2012). RNA-seq assembly - are we there yet? Frontiers in Plant Science 3:220.
Schliesky, S., et al., 2012. RNA-seq assembly - are we there yet? Frontiers in Plant Science, 3: 220.
S. Schliesky, et al., “RNA-seq assembly - are we there yet?”, Frontiers in Plant Science, vol. 3, 2012, : 220.
Schliesky, S., Gowik, U., Weber, A.P.M., Bräutigam, A.: RNA-seq assembly - are we there yet? Frontiers in Plant Science. 3, : 220 (2012).
Schliesky, Simon, Gowik, Udo, Weber, Andreas P. M., and Bräutigam, Andrea. “RNA-seq assembly - are we there yet?”. Frontiers in Plant Science 3 (2012): 220.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Copyright Statement:
This Item is protected by copyright and/or related rights. [...]
Access Level
OA Open Access
Zuletzt Hochgeladen

42 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

454 pyrosequencing-based analysis of gene expression profiles in the amphipod Melita plumulosa: transcriptome assembly and toxicant induced changes.
Hook SE, Twine NA, Simpson SL, Spadaro DA, Moncuquet P, Wilkins MR., Aquat Toxicol 153(), 2014
PMID: 24434169
Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data.
Lohse M, Nagel A, Herter T, May P, Schroda M, Zrenner R, Tohge T, Fernie AR, Stitt M, Usadel B., Plant Cell Environ 37(5), 2014
PMID: 24237261
RNA-Seq analysis of the toxicant-induced transcriptome of the marine diatom, Ceratoneis closterium.
Hook SE, Osborn HL, Gissi F, Moncuquet P, Twine NA, Wilkins MR, Adams MS., Mar Genomics 16(), 2014
PMID: 24393604
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
The metal transporter PgIREG1 from the hyperaccumulator Psychotria gabriellae is a candidate gene for nickel tolerance and accumulation.
Merlot S, Hannibal L, Martins S, Martinelli L, Amir H, Lebrun M, Thomine S., J Exp Bot 65(6), 2014
PMID: 24510940
The use of versatile plant antimicrobial peptides in agribusiness and human health.
de Souza Cândido E, e Silva Cardoso MH, Sousa DA, Viana JC, de Oliveira-Júnior NG, Miranda V, Franco OL., Peptides 55(), 2014
PMID: 24548568
Fuelling genetic and metabolic exploration of C3 bioenergy crops through the first reference transcriptome of Arundo donax L.
Sablok G, Fu Y, Bobbio V, Laura M, Rotino GL, Bagnaresi P, Allavena A, Velikova V, Viola R, Loreto F, Li M, Varotto C., Plant Biotechnol J 12(5), 2014
PMID: PMC4285118
RNA-Seq data: a goldmine for organelle research.
Smith DR., Brief Funct Genomics 12(5), 2013
PMID: 23334532
Comparative analysis of de novo transcriptome assembly.
Clarke K, Yang Y, Marsh R, Xie L, Zhang KK., Sci China Life Sci 56(2), 2013
PMID: 23393031
The plant transcriptome-from integrating observations to models.
Usadel B, Fernie AR., Front Plant Sci 4(), 2013
PMID: 23483867
Catalyzing plant science research with RNA-seq.
Martin LB, Fei Z, Giovannoni JJ, Rose JK., Front Plant Sci 4(), 2013
PMID: 23554602
Glycyrrhiza uralensis transcriptome landscape and study of phytochemicals.
Ramilowski JA, Sawai S, Seki H, Mochida K, Yoshida T, Sakurai T, Muranaka T, Saito K, Daub CO., Plant Cell Physiol 54(5), 2013
PMID: 23589666
Transcriptome analysis based on next-generation sequencing of non-model plants producing specialized metabolites of biotechnological interest.
Xiao M, Zhang Y, Chen X, Lee EJ, Barber CJ, Chakrabarty R, Desgagné-Penix I, Haslam TM, Kim YB, Liu E, MacNevin G, Masada-Atsumi S, Reed DW, Stout JM, Zerbe P, Zhang Y, Bohlmann J, Covello PS, De Luca V, Page JE, Ro DK, Martin VJ, Facchini PJ, Sensen CW., J Biotechnol 166(3), 2013
PMID: 23602801
A contribution to the study of plant development evolution based on gene co-expression networks.
Romero-Campero FJ, Lucas-Reina E, Said FE, Romero JM, Valverde F., Front Plant Sci 4(), 2013
PMID: 23935602

43 References

Daten bereitgestellt von Europe PubMed Central.

De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq.
Mizrachi E, Hefer CA, Ranik M, Joubert F, Myburg AA., BMC Genomics 11(), 2010
PMID: 21122097
High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome.
Novaes E, Drost DR, Farmerie WG, Pappas GJ Jr, Grattapaglia D, Sederoff RR, Kirst M., BMC Genomics 9(), 2008
PMID: 18590545
An Eulerian path approach to DNA fragment assembly.
Pevzner PA, Tang H, Waterman MS., Proc. Natl. Acad. Sci. U.S.A. 98(17), 2001
PMID: 11504945
RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.).
Pont C, Murat F, Confolent C, Balzergue S, Salse J., Genome Biol. 12(12), 2011
PMID: 22136458
Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds.
Shi CY, Yang H, Wei CL, Yu O, Zhang ZZ, Jiang CJ, Sun J, Li YY, Chen Q, Xia T, Wan XC., BMC Genomics 12(), 2011
PMID: 21356090
ABySS: a parallel assembler for short read sequence data.
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I., Genome Res. 19(6), 2009
PMID: 19251739
An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNA-seq and digital gene expression analysis.
Tang Q, Ma X, Mo C, Wilson IW, Song C, Zhao H, Yang Y, Fu W, Qiu D., BMC Genomics 12(), 2011
PMID: 21729270
Comparative deep transcriptional profiling of four developing oilseeds.
Troncoso-Ponce MA, Kilaru A, Cao X, Durrett TP, Fan J, Jensen JK, Thrower NA, Pauly M, Wilkerson C, Ohlrogge JB., Plant J. 68(6), 2011
PMID: 21851431
Deep sampling of the Palomero maize transcriptome by a high throughput strategy of pyrosequencing.
Vega-Arreguin JC, Ibarra-Laclette E, Jimenez-Moraila B, Martinez O, Vielle-Calzada JP, Herrera-Estrella L, Herrera-Estrella A., BMC Genomics 10(), 2009
PMID: 19580677
RNA-Seq reveals genotype-specific molecular responses to water deficit in eucalyptus.
Villar E, Klopp C, Noirot C, Novaes E, Kirst M, Plomion C, Gion JM., BMC Genomics 12(), 2011
PMID: 22047139
Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database.
Blavet N, Charif D, Oger-Desfeux C, Marais GA, Widmer A., BMC Genomics 12(), 2011
PMID: 21791039
Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Zerbino DR, Birney E., Genome Res. 18(5), 2008
PMID: 18349386
De novo assembly and characterisation of the transcriptome during seed development, and generation of genic-SSR markers in peanut (Arachis hypogaea L.).
Zhang J, Liang S, Duan J, Wang J, Chen S, Cheng Z, Zhang Q, Liang X, Li Y., BMC Genomics 13(), 2012
PMID: 22409576
RNA-seq discovery, functional characterization, and comparison of sesquiterpene synthases from Solanum lycopersicum and Solanum habrochaites trichomes.
Bleeker PM, Spyropoulou EA, Diergaarde PJ, Volpin H, De Both MT, Zerbe P, Bohlmann J, Falara V, Matsuba Y, Pichersky E, Haring MA, Schuurink RC., Plant Mol. Biol. 77(4-5), 2011
PMID: 21818683
An mRNA blueprint for C4 photosynthesis derived from comparative transcriptomics of closely related C3 and C4 species.
Brautigam 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


Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®


PMID: 23056003
PubMed | Europe PMC

Suchen in

Google Scholar