High efficiency application of a mate-paired library from next-generation sequencing to postlight sequencing: Corynebacterium pseudotuberculosis as a case study for microbial de novo genome assembly

Ramos RTJ, Carneiro AR, de Castro Soares S, Barbosa S, Varuzza L, Orabona G, Tauch A, Azevedo V, Schneider MP, Silva A (2013)
Journal of microbiological methods 95(3): 441-447.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Autor*in
Ramos, Rommel Thiago Jucá; Carneiro, Adriana Ribeiro; de Castro Soares, Siomar; Barbosa, Silvanira; Varuzza, Leonardo; Orabona, Guilherme; Tauch, AndreasUniBi; Azevedo, Vasco; Schneider, Maria Paula; Silva, Artur
Abstract / Bemerkung
With the advent of high-throughput DNA sequencing platforms, there has been a reduction in the cost and time of sequencing. With these advantages, new challenges have emerged, such as the handling of large amounts of data, quality assessment, and the assembly of short reads. Currently, benchtop high-throughput sequencers enable the genomes of prokaryotic organisms to be sequenced within two hours with a reduction in coverage compared with the SOLiD, Illumina and 454 FLX Titanium platforms, making it necessary to evaluate the efficiency of less expensive benchtop instruments for prokaryotic genomics. In the present work, we evaluate and propose a methodology for the use of the Ion Torrent PGM platform for decoding the gram-positive bacterium Corynebacterium pseudotuberculosis, for which 15 complete genome sequences have already been deposited based on fragment and mate-paired libraries with a 3-kb insert size. Despite the low coverage, a single sequencing run using a mate-paired library generated 39 scaffolds after de novo assembly without data curation. This result is superior to that obtained by sequencing using libraries generated from fragments marketed by the equipment's manufacturer, as well as that observed for mate-pairs sequenced by SOLiD. The generated sequence added an extra 91kb to the genome available at NCBI.
Erscheinungsjahr
2013
Zeitschriftentitel
Journal of microbiological methods
Band
95
Ausgabe
3
Seite(n)
441-447
ISSN
0167-7012
Page URI
https://pub.uni-bielefeld.de/record/2641278

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Ramos RTJ, Carneiro AR, de Castro Soares S, et al. High efficiency application of a mate-paired library from next-generation sequencing to postlight sequencing: Corynebacterium pseudotuberculosis as a case study for microbial de novo genome assembly. Journal of microbiological methods. 2013;95(3):441-447.
Ramos, R. T. J., Carneiro, A. R., de Castro Soares, S., Barbosa, S., Varuzza, L., Orabona, G., Tauch, A., et al. (2013). High efficiency application of a mate-paired library from next-generation sequencing to postlight sequencing: Corynebacterium pseudotuberculosis as a case study for microbial de novo genome assembly. Journal of microbiological methods, 95(3), 441-447. https://doi.org/10.1016/j.mimet.2013.06.006
Ramos, R. T. J., Carneiro, A. R., de Castro Soares, S., Barbosa, S., Varuzza, L., Orabona, G., Tauch, A., Azevedo, V., Schneider, M. P., and Silva, A. (2013). High efficiency application of a mate-paired library from next-generation sequencing to postlight sequencing: Corynebacterium pseudotuberculosis as a case study for microbial de novo genome assembly. Journal of microbiological methods 95, 441-447.
Ramos, R.T.J., et al., 2013. High efficiency application of a mate-paired library from next-generation sequencing to postlight sequencing: Corynebacterium pseudotuberculosis as a case study for microbial de novo genome assembly. Journal of microbiological methods, 95(3), p 441-447.
R.T.J. Ramos, et al., “High efficiency application of a mate-paired library from next-generation sequencing to postlight sequencing: Corynebacterium pseudotuberculosis as a case study for microbial de novo genome assembly”, Journal of microbiological methods, vol. 95, 2013, pp. 441-447.
Ramos, R.T.J., Carneiro, A.R., de Castro Soares, S., Barbosa, S., Varuzza, L., Orabona, G., Tauch, A., Azevedo, V., Schneider, M.P., Silva, A.: High efficiency application of a mate-paired library from next-generation sequencing to postlight sequencing: Corynebacterium pseudotuberculosis as a case study for microbial de novo genome assembly. Journal of microbiological methods. 95, 441-447 (2013).
Ramos, Rommel Thiago Jucá, Carneiro, Adriana Ribeiro, de Castro Soares, Siomar, Barbosa, Silvanira, Varuzza, Leonardo, Orabona, Guilherme, Tauch, Andreas, Azevedo, Vasco, Schneider, Maria Paula, and Silva, Artur. “High efficiency application of a mate-paired library from next-generation sequencing to postlight sequencing: Corynebacterium pseudotuberculosis as a case study for microbial de novo genome assembly”. Journal of microbiological methods 95.3 (2013): 441-447.

4 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Rapidly evolving changes and gene loss associated with host switching in Corynebacterium pseudotuberculosis.
Viana MVC, Sahm A, Góes Neto A, Figueiredo HCP, Wattam AR, Azevedo V., PLoS One 13(11), 2018
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Comparative genomic analysis between Corynebacterium pseudotuberculosis strains isolated from buffalo.
Viana MVC, Figueiredo H, Ramos R, Guimarães LC, Pereira FL, Dorella FA, Selim SAK, Salaheldean M, Silva A, Wattam AR, Azevedo V., PLoS One 12(4), 2017
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Whole-genome optical mapping reveals a mis-assembly between two rRNA operons of Corynebacterium pseudotuberculosis strain 1002.
Mariano DC, Sousa Tde J, Pereira FL, Aburjaile F, Barh D, Rocha F, Pinto AC, Hassan SS, Saraiva TD, Dorella FA, de Carvalho AF, Leal CA, Figueiredo HC, Silva A, Ramos RT, Azevedo VA., BMC Genomics 17(), 2016
PMID: 27129708
Draft Genome Sequence of Haloferax sp. Strain ATB1, Isolated from a Semi-Arid Region in the Brazilian Caatinga.
Castro Wde O, Torres-Ballesteros AM, Nakayama CR, Melo IS, Pellizari VH, Silva A, Ramos RT., Genome Announc 2(4), 2014
PMID: 25125649

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