Sequencing of high G + C microbial genomes using the ultrafast pyrosequencing technology

Schwientek P, Szczepanowski R, Rückert C, Stoye J, Pühler A (2011)
Journal of Biotechnology 155(1): 68-77.

Download
No fulltext has been uploaded. References only!
Journal Article | Original Article | Published | English

No fulltext has been uploaded

Abstract / Notes
Next generation pyrosequencing of high G+C content genomes still poses problems to automated sequencing and assembly processes which necessitates cost and time intensive manual work in order to finish such genomes completely. The sequencing of the high G+C actinomycete Actinoplanes sp. SE50/110 was performed with standard pyrosequencing technology (454 Life Sciences) and revealed a high number of gaps. The reasons for the introduction of gaps were analyzed on a previously known 41kb long DNA reference sequence from Actinoplanes sp. SE50/110, hosting the acarbose biosynthesis gene cluster. Mapping of the sequencing results on the reference gene cluster sequence revealed a fragmentation into 30 contiguous sequences of different lengths. The gaps between these sequences were characterized by extremely low read coverage which strongly correlated with the G+C content in the gap regions in a negative manner. Furthermore, the gap-sequences contained strong stem-loop structures which hindered the amplification of these sequences during the emulsion PCR. Being significantly underrepresented or absent in the subsequent sequencing process, these sequences lead to weakly or uncovered genomic regions which forces the assembly algorithm to output multiple contiguous sequences instead of one finished genome. However, by applying a different pyrosequencing protocol, it was possible to sequence the complete acarbose biosynthesis gene cluster. The changes to the protocol include longer read length and addition of chemicals to the amplification chemistry, which reduces the self-annealing of DNA fragments during the amplification process and enables the complete reconstruction of high G+C content genomes without manual intervention. Copyright 2011 Elsevier B.V. All rights reserved.
Publishing Year
ISSN
PUB-ID

Cite this

Schwientek P, Szczepanowski R, Rückert C, Stoye J, Pühler A. Sequencing of high G + C microbial genomes using the ultrafast pyrosequencing technology. Journal of Biotechnology. 2011;155(1):68-77.
Schwientek, P., Szczepanowski, R., Rückert, C., Stoye, J., & Pühler, A. (2011). Sequencing of high G + C microbial genomes using the ultrafast pyrosequencing technology. Journal of Biotechnology, 155(1), 68-77. doi:10.1016/j.jbiotec.2011.04.010
Schwientek, P., Szczepanowski, R., Rückert, C., Stoye, J., and Pühler, A. (2011). Sequencing of high G + C microbial genomes using the ultrafast pyrosequencing technology. Journal of Biotechnology 155, 68-77.
Schwientek, P., et al., 2011. Sequencing of high G + C microbial genomes using the ultrafast pyrosequencing technology. Journal of Biotechnology, 155(1), p 68-77.
P. Schwientek, et al., “Sequencing of high G + C microbial genomes using the ultrafast pyrosequencing technology”, Journal of Biotechnology, vol. 155, 2011, pp. 68-77.
Schwientek, P., Szczepanowski, R., Rückert, C., Stoye, J., Pühler, A.: Sequencing of high G + C microbial genomes using the ultrafast pyrosequencing technology. Journal of Biotechnology. 155, 68-77 (2011).
Schwientek, Patrick, Szczepanowski, Rafael, Rückert, Christian, Stoye, Jens, and Pühler, Alfred. “Sequencing of high G + C microbial genomes using the ultrafast pyrosequencing technology”. Journal of Biotechnology 155.1 (2011): 68-77.
This data publication is cited in the following publications:
This publication cites the following data publications:

24 Citations in Europe PMC

Data provided by Europe PubMed Central.

Genome improvement of the acarbose producer Actinoplanes sp. SE50/110 and annotation refinement based on RNA-seq analysis.
Wolf T, Schneiker-Bekel S, Neshat A, Ortseifen V, Wibberg D, Zemke T, Pühler A, Kalinowski J., J Biotechnol 251(), 2017
PMID: 28427920
Complete genome sequence of the actinobacterium Streptomyces glaucescens GLA.O (DSM 40922) consisting of a linear chromosome and one linear plasmid.
Ortseifen V, Winkler A, Albersmeier A, Wendler S, Pühler A, Kalinowski J, Rückert C., J Biotechnol 194(), 2015
PMID: 25499805
Complete genome sequence of Streptomyces lividans TK24.
Rückert C, Albersmeier A, Busche T, Jaenicke S, Winkler A, Friðjónsson ÓH, Hreggviðsson GÓ, Lambert C, Badcock D, Bernaerts K, Anne J, Economou A, Kalinowski J., J Biotechnol 199(), 2015
PMID: 25680930
Comprehensive proteome analysis of Actinoplanes sp. SE50/110 highlighting the location of proteins encoded by the acarbose and the pyochelin biosynthesis gene cluster.
Wendler S, Otto A, Ortseifen V, Bonn F, Neshat A, Schneiker-Bekel S, Walter F, Wolf T, Zemke T, Wehmeier UF, Hecker M, Kalinowski J, Becher D, Pühler A., J Proteomics 125(), 2015
PMID: 25896738
The Sinorhizobium fredii HH103 Genome: A Comparative Analysis With S. fredii Strains Differing in Their Symbiotic Behavior With Soybean.
Vinardell JM, Acosta-Jurado S, Zehner S, Göttfert M, Becker A, Baena I, Blom J, Crespo-Rivas JC, Goesmann A, Jaenicke S, Krol E, McIntosh M, Margaret I, Pérez-Montaño F, Schneiker-Bekel S, Serranía J, Szczepanowski R, Buendía AM, Lloret J, Bonilla I, Pühler A, Ruiz-Sainz JE, Weidner S., Mol Plant Microbe Interact 28(7), 2015
PMID: 25675256
The human oral metaproteome reveals potential biomarkers for caries disease.
Belda-Ferre P, Williamson J, Simón-Soro Á, Artacho A, Jensen ON, Mira A., Proteomics 15(20), 2015
PMID: 26272225
Draft Genome Sequence of Streptomyces niveus NCIMB 11891, Producer of the Aminocoumarin Antibiotic Novobiocin.
Flinspach K, Rückert C, Kalinowski J, Heide L, Apel AK., Genome Announc 2(1), 2014
PMID: 24407644
Complete genome sequence of the actinobacterium Actinoplanes friuliensis HAG 010964, producer of the lipopeptide antibiotic friulimycin.
Rückert C, Szczepanowski R, Albersmeier A, Goesmann A, Fischer N, Steinkämper A, Pühler A, Biener R, Schwartz D, Kalinowski J., J Biotechnol 178(), 2014
PMID: 24637369
Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts.
Schwientek P, Neshat A, Kalinowski J, Klein A, Rückert C, Schneiker-Bekel S, Wendler S, Stoye J, Pühler A., J Biotechnol 190(), 2014
PMID: 24642337
Carbon source dependent biosynthesis of acarviose metabolites in Actinoplanes sp. SE50/110.
Wendler S, Ortseifen V, Persicke M, Klein A, Neshat A, Niehaus K, Schneiker-Bekel S, Walter F, Wehmeier UF, Kalinowski J, Pühler A., J Biotechnol 191(), 2014
PMID: 25169663
Complete genome sequence of Corynebacterium casei LMG S-19264T (=DSM 44701T), isolated from a smear-ripened cheese.
Walter F, Albersmeier A, Kalinowski J, Rückert C., J Biotechnol 189(), 2014
PMID: 25193709
Complete genome sequence of Corynebacterium vitaeruminis DSM 20294T, isolated from the cow rumen as a vitamin B producer.
Al-Dilaimi A, Albersmeier A, Kalinowski J, Rückert C., J Biotechnol 189(), 2014
PMID: 25193714
Complete genome sequence of the actinobacterium Amycolatopsis japonica MG417-CF17(T) (=DSM 44213T) producing (S,S)-N,N'-ethylenediaminedisuccinic acid.
Stegmann E, Albersmeier A, Spohn M, Gert H, Weber T, Wohlleben W, Kalinowski J, Rückert C., J Biotechnol 189(), 2014
PMID: 25193710
Complete genome sequence of producer of the glycopeptide antibiotic Aculeximycin Kutzneria albida DSM 43870T, a representative of minor genus of Pseudonocardiaceae.
Rebets Y, Tokovenko B, Lushchyk I, Rückert C, Zaburannyi N, Bechthold A, Kalinowski J, Luzhetskyy A., BMC Genomics 15(), 2014
PMID: 25301375
Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media.
Schwientek P, Wendler S, Neshat A, Eirich C, Rückert C, Klein A, Wehmeier UF, Kalinowski J, Stoye J, Pühler A., J Biotechnol 167(2), 2013
PMID: 23142701
Sequencing platform and library preparation choices impact viral metagenomes.
Solonenko SA, Ignacio-Espinoza JC, Alberti A, Cruaud C, Hallam S, Konstantinidis K, Tyson G, Wincker P, Sullivan MB., BMC Genomics 14(), 2013
PMID: 23663384
Complete genome sequence of the kirromycin producer Streptomyces collinus Tü 365 consisting of a linear chromosome and two linear plasmids.
Rückert C, Szczepanowski R, Albersmeier A, Goesmann A, Iftime D, Musiol EM, Blin K, Wohlleben W, Pühler A, Kalinowski J, Weber T., J Biotechnol 168(4), 2013
PMID: 24140291
The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110.
Schwientek P, Szczepanowski R, Rückert C, Kalinowski J, Klein A, Selber K, Wehmeier UF, Stoye J, Pühler A., BMC Genomics 13(), 2012
PMID: 22443545
Draft genome sequence of Corynebacterium bovis DSM 20582, which causes clinical mastitis in dairy cows.
Schröder J, Glaub A, Schneider J, Trost E, Tauch A., J Bacteriol 194(16), 2012
PMID: 22843578
Genome sequence of the bacterium Streptomyces davawensis JCM 4913 and heterologous production of the unique antibiotic roseoflavin.
Jankowitsch F, Schwarz J, Rückert C, Gust B, Szczepanowski R, Blom J, Pelzer S, Kalinowski J, Mack M., J Bacteriol 194(24), 2012
PMID: 23043000
A bacterial glycosidase enables mannose-6-phosphate modification and improved cellular uptake of yeast-produced recombinant human lysosomal enzymes.
Tiels P, Baranova E, Piens K, De Visscher C, Pynaert G, Nerinckx W, Stout J, Fudalej F, Hulpiau P, Tännler S, Geysens S, Van Hecke A, Valevska A, Vervecken W, Remaut H, Callewaert N., Nat Biotechnol 30(12), 2012
PMID: 23159880

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 21536083
PubMed | Europe PMC

Search this title in

Google Scholar