Improvement in the DNA sequencing of genomes bearing long repeated elements
- PMID:25447886
- DOI: 10.1016/j.mimet.2014.10.016
Improvement in the DNA sequencing of genomes bearing long repeated elements
Abstract
When using next-generation sequencing methods, obtaining a single and complete bacterial chromosomic sequence may be challenging especially for bacteria harboring multiple repeated sequences. Here we present a one-step procedure to optimize the sequencing process in order to obtain a single chromosomic scaffold.
Copyright © 2014 Elsevier B.V. All rights reserved.
Similar articles
- Sequencing of high G+C microbial genomes using the ultrafast pyrosequencing technology.Schwientek P, Szczepanowski R, Rückert C, Stoye J, Pühler A.Schwientek P, et al.J Biotechnol. 2011 Aug 20;155(1):68-77. doi: 10.1016/j.jbiotec.2011.04.010. Epub 2011 Apr 23.J Biotechnol. 2011.PMID:21536083
- Next-generation sequencing technologies and their impact on microbial genomics.Forde BM, O'Toole PW.Forde BM, et al.Brief Funct Genomics. 2013 Sep;12(5):440-53. doi: 10.1093/bfgp/els062. Epub 2013 Jan 11.Brief Funct Genomics. 2013.PMID:23314033Review.
- Bacterial Genomic Data Analysis in the Next-Generation Sequencing Era.Orsini M, Cuccuru G, Uva P, Fotia G.Orsini M, et al.Methods Mol Biol. 2016;1415:407-22. doi: 10.1007/978-1-4939-3572-7_21.Methods Mol Biol. 2016.PMID:27115645
- Whole-genome sequencing for comparative genomics and de novo genome assembly.Benjak A, Sala C, Hartkoorn RC.Benjak A, et al.Methods Mol Biol. 2015;1285:1-16. doi: 10.1007/978-1-4939-2450-9_1.Methods Mol Biol. 2015.PMID:25779307
- Sequence assembly.Scheibye-Alsing K, Hoffmann S, Frankel A, Jensen P, Stadler PF, Mang Y, Tommerup N, Gilchrist MJ, Nygård AB, Cirera S, Jørgensen CB, Fredholm M, Gorodkin J.Scheibye-Alsing K, et al.Comput Biol Chem. 2009 Apr;33(2):121-36. doi: 10.1016/j.compbiolchem.2008.11.003. Epub 2008 Dec 6.Comput Biol Chem. 2009.PMID:19152793Review.
Cited by
- Diversity of antibiotic-resistance genes in Canadian isolates of Aeromonas salmonicida subsp. salmonicida: dominance of pSN254b and discovery of pAsa8.Trudel MV, Vincent AT, Attéré SA, Labbé M, Derome N, Culley AI, Charette SJ.Trudel MV, et al.Sci Rep. 2016 Oct 18;6:35617. doi: 10.1038/srep35617.Sci Rep. 2016.PMID:27752114Free PMC article.
- Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida.Vincent AT, Trudel MV, Freschi L, Nagar V, Gagné-Thivierge C, Levesque RC, Charette SJ.Vincent AT, et al.BMC Genomics. 2016 Jan 12;17:44. doi: 10.1186/s12864-016-2381-3.BMC Genomics. 2016.PMID:26753691Free PMC article.
- The mosaic architecture ofAeromonas salmonicida subsp.salmonicida pAsa4 plasmid and its consequences on antibiotic resistance.Tanaka KH, Vincent AT, Trudel MV, Paquet VE, Frenette M, Charette SJ.Tanaka KH, et al.PeerJ. 2016 Oct 27;4:e2595. doi: 10.7717/peerj.2595. eCollection 2016.PeerJ. 2016.PMID:27812409Free PMC article.
- Diversity and Homogeneity among Small Plasmids of Aeromonas salmonicida subsp. salmonicida Linked with Geographical Origin.Attéré SA, Vincent AT, Trudel MV, Chanut R, Charette SJ.Attéré SA, et al.Front Microbiol. 2015 Nov 23;6:1274. doi: 10.3389/fmicb.2015.01274. eCollection 2015.Front Microbiol. 2015.PMID:26635745Free PMC article.
- Completion of genome ofAeromonas salmonicida subsp.salmonicida 01-B526 reveals how sequencing technologies can influence sequence quality and result interpretations.Vincent AT, Charette SJ.Vincent AT, et al.New Microbes New Infect. 2018 May 31;25:24-26. doi: 10.1016/j.nmni.2018.05.007. eCollection 2018 Sep.New Microbes New Infect. 2018.PMID:29983988Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
Other Literature Sources