Identifying microbial species by single-molecule DNA optical mapping and resampling statistics.
Journal
NAR genomics and bioinformatics
ISSN: 2631-9268
Titre abrégé: NAR Genom Bioinform
Pays: England
ID NLM: 101756213
Informations de publication
Date de publication:
Mar 2020
Mar 2020
Historique:
received:
30
08
2019
accepted:
12
09
2019
entrez:
12
2
2021
pubmed:
5
10
2019
medline:
5
10
2019
Statut:
epublish
Résumé
Single-molecule DNA mapping has the potential to serve as a powerful complement to high-throughput sequencing in metagenomic analysis. Offering longer read lengths and forgoing the need for complex library preparation and amplification, mapping stands to provide an unbiased view into the composition of complex viromes and/or microbiomes. To fully enable mapping-based metagenomics, sensitivity and specificity of DNA map analysis and identification need to be improved. Using detailed simulations and experimental data, we first demonstrate how fluorescence imaging of surface stretched, sequence specifically labeled DNA fragments can yield highly sensitive identification of targets. Second, a new analysis technique is introduced to increase specificity of the analysis, allowing even closely related species to be resolved. Third, we show how an increase in resolution improves sensitivity. Finally, we demonstrate that these methods are capable of identifying species with long genomes such as bacteria with high sensitivity.
Identifiants
pubmed: 33575560
doi: 10.1093/nargab/lqz007
pii: lqz007
pmc: PMC7671359
doi:
Types de publication
Journal Article
Langues
eng
Pagination
lqz007Informations de copyright
© The Author(s) 2019. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.
Références
Nucleic Acids Res. 2014 Apr;42(7):e50
pubmed: 24452797
J Am Chem Soc. 2007 Mar 14;129(10):2758-9
pubmed: 17309265
Nature. 2012 Jun 13;486(7402):207-14
pubmed: 22699609
PLoS One. 2013;8(1):e53671
pubmed: 23382848
Nucleic Acids Res. 2016 Jan 29;44(2):e11
pubmed: 26481349
ACS Nano. 2016 Jan 26;10(1):6-37
pubmed: 26695070
Nucleic Acids Res. 2015 Oct 15;43(18):e117
pubmed: 26019180
Curr Opin Gastroenterol. 2015 Jan;31(1):69-75
pubmed: 25394236
Biochem Biophys Res Commun. 2012 Jan 6;417(1):404-8
pubmed: 22166208
Nucleic Acids Res. 2019 Jul 9;47(12):e68
pubmed: 30918971
Biotechniques. 2017 Jun 1;62(6):255-267
pubmed: 28625155
Science. 1988 Jun 3;240(4857):1285-93
pubmed: 3287615
ACS Nano. 2015 Jan 27;9(1):809-16
pubmed: 25561163
Bioinformatics. 2016 Apr 1;32(7):1016-22
pubmed: 26637292
J Microsc. 2000 May;198(Pt 2):82-7
pubmed: 10810003
Sci Rep. 2016 Jul 27;6:30410
pubmed: 27460437
Proc Natl Acad Sci U S A. 2017 Jul 25;114(30):E6166-E6175
pubmed: 28696303
Gigascience. 2014 Dec 30;3(1):33
pubmed: 25671093
Biopolymers. 2011 May;95(5):298-311
pubmed: 21207457
Nucleic Acids Res. 2018 Jun 20;46(11):e64
pubmed: 29546351
Viruses. 2017 May 24;9(6):
pubmed: 28538703
Nucleic Acids Res. 2014 Sep;42(15):e118
pubmed: 25013180
Nat Rev Genet. 2012 Mar 13;13(4):260-70
pubmed: 22411464
Proc Natl Acad Sci U S A. 2010 Jul 27;107(30):13294-9
pubmed: 20616076
Angew Chem Int Ed Engl. 2017 May 2;56(19):5182-5200
pubmed: 27943567
Proc Natl Acad Sci U S A. 2006 Oct 24;103(43):15770-5
pubmed: 17043225
Nat Commun. 2016 Mar 21;7:10980
pubmed: 26996201
PLoS Comput Biol. 2012;8(11):e1002779
pubmed: 23209389
Genome Res. 2008 Nov;18(11):1851-8
pubmed: 18714091
J Med Virol. 2016 Sep;88(9):1467-72
pubmed: 26919534
Proc Natl Acad Sci U S A. 2018 Oct 30;115(44):11192-11197
pubmed: 30322920
J Comput Biol. 2006 Mar;13(2):442-62
pubmed: 16597251
Science. 1994 Sep 30;265(5181):2096-8
pubmed: 7522347
Microbiol Rev. 1995 Mar;59(1):143-69
pubmed: 7535888
Annu Rev Microbiol. 2003;57:369-94
pubmed: 14527284