Implementation and Data Analysis of Tn-seq, Whole-Genome Resequencing, and Single-Molecule Real-Time Sequencing for Bacterial Genetics.
Few discoveries have been more transformative to the biological sciences than the development of DNA sequencing technologies. The rapid advancement of sequencing and bioinformatics tools has revolutionized bacterial genetics, deepening our understanding of model and clinically relevant organisms. Although application of newer sequencing technologies to studies in bacterial genetics is increasing, the implementation of DNA sequencing technologies and development of the bioinformatics tools required for analyzing the large data sets generated remain a challenge for many. In this minireview, we have chosen to summarize three sequencing approaches that are particularly useful for bacterial genetics. We provide resources for scientists new to and interested in their application. Here, we discuss the analysis of data from transposon mutagenesis followed by deep sequencing (Tn-seq) to determine gene disruptions differentially represented in a mutant population and Illumina sequencing for identification of suppressor or other mutations, and we summarize single-molecule real-time (SMRT) sequencing for de novo genome assembly and the use of the output data for detection of DNA base modifications.
Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
Peter E
PE
Burby
Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
Taylor M
TM
Nye
Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
Jeremy W
JW
Schroeder
Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA lasimm@umich.edu.
Lyle A
LA
Simmons
D001419:Bacteria / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology; D016680:Genome, Bacterial; D009154:Mutation; D021141:Nucleic Acid Amplification Techniques
D004269:DNA, Bacterial
High-throughput; SMRT; Tn-seq; sequencing
Appl Microbiol Biotechnol. 2016 Jan;100(1):31-43
26476650
Proc Natl Acad Sci U S A. 2014 Nov 18;111(46):16454-9
25368150
Curr Biol. 2016 Mar 7;26(5):692-7
26923786
Genome Res. 2008 Nov;18(11):1851-8
18714091
Bioinformatics. 2010 Jan 1;26(1):139-40
19910308
J Mol Biol. 1962 Jul;5:18-36
13862047
Curr Opin Microbiol. 2015 Feb;23:133-40
25483350
Radiat Res. 1995 Jun;142(3):362-8
7761586
Nat Rev Microbiol. 2013 Jul;11(7):435-42
23712350
Science. 2003 Jan 31;299(5607):682-6
12560545
Curr Opin Microbiol. 2015 Feb;23:110-20
25461581
MBio. 2011 Jan 18;2(1):e00315-10
21253457
PLoS Genet. 2016 Feb 12;12(2):e1005854
26870957
Front Microbiol. 2014 Jun 24;5:305
25009536
Genome Biol. 2010;11(10):R106
20979621
Microbiol Spectr. 2014 Apr;2(2):null
26105820
Mol Cell. 2003 Oct;12(4):947-57
14580345
J Bacteriol. 2014 Oct;196(20):3534-45
25049088
Genome Announc. 2013 Dec 19;1(6):null
24356846
Mol Cell. 2006 Nov 17;24(4):581-92
17114060
Curr Opin Microbiol. 2013 Apr;16(2):192-8
23434113
Proc Natl Acad Sci U S A. 2013 Feb 12;110(7):2623-8
23362380
Bioinformatics. 2009 Aug 15;25(16):2078-9
19505943
Nat Rev Microbiol. 2003 Nov;1(2):117-26
15035041
Science. 2009 Jan 2;323(5910):133-8
19023044
Science. 1995 Jul 28;269(5223):496-512
7542800
Mutat Res. 1979 Feb;59(2):157-65
375073
Nucleic Acids Res. 2015 Jan;43(Database issue):D298-9
25378308
J Mol Biol. 1982 Dec 25;162(4):729-73
6221115
Nat Biotechnol. 2012 Jul 01;30(7):701-7
22750883
Genetics. 1983 Aug;104(4):571-82
6225697
Chembiochem. 2002 Apr 2;3(4):274-93
11933228
Bioinformatics. 2009 Nov 1;25(21):2841-2
19736251
Nat Genet. 2011 May;43(5):491-8
21478889
Nat Genet. 2014 Jan;46(1):82-7
24316980
Bioinformatics. 2009 Jun 1;25(11):1363-9
19357099
MBio. 2015 May 12;6(3):e00306-15
25968644
Nat Rev Genet. 2013 Jun;14(6):390-403
23657480
J Biol Chem. 2004 Jul 16;279(29):30236-43
15151991
Proc Natl Acad Sci U S A. 2009 Sep 22;106(38):16422-7
19805314
Nat Methods. 2010 Jun;7(6):461-5
20453866
Lancet Infect Dis. 2016 Feb;16(2):161-8
26603172
Nat Commun. 2014 Sep 30;5:5055
25268848
Proc Natl Acad Sci U S A. 1968 Apr;59(4):1300-6
4870862
PLoS Biol. 2016 Jan 06;14(1):e1002341
26735940
Gene. 2016 Jul 25;586(2):239-47
27063562
Nat Protoc. 2011 Nov 17;6(12):1969-80
22094732
Sci Rep. 2016 May 09;6:25533
27156886
J Mol Biol. 1978 Oct 25;125(2):225-46
731693
Genome Biol. 2013;14(9):R101
24034426
Nat Methods. 2009 Oct;6(10):767-72
19767758
J Biol Chem. 2013 May 17;288(20):13929-35
23592777
Genome Res. 2009 Dec;19(12):2308-16
19826075
Microbiome. 2015 Oct 05;3:43
26434730
PLoS One. 2015 May 22;10(5):e0128036
26000737
Nucleic Acids Res. 2010 Aug;38(15):e159
20571086
Genome Res. 2012 Dec;22(12):2541-51
22826510
Annu Rev Genet. 1996;30:297-41
8982457
Bioinformatics. 2009 Jul 15;25(14):1754-60
19451168
Nat Methods. 2009 Sep;6(9):677-81
19668202
Nucleic Acids Res. 2014 Apr;42(6):3720-35
24398711
FEMS Microbiol Rev. 2009 May;33(3):488-503
19175412
Nat Methods. 2015 Mar;12(3):203-6, 4 p following 206
25559584
DNA Repair (Amst). 2015 Aug;32:86-95
26003632
Genes Dev. 2011 Jun 15;25(12):1328-43
21685367
Curr Protoc Mol Biol. 2011 Oct;Chapter 7:Unit7.1
21987056
Nucleic Acids Res. 2015 Feb 18;43(3):e19
25428359
J Bacteriol. 2014 Apr;196(7):1359-68
24443534
Cell Host Microbe. 2009 Sep 17;6(3):279-89
19748469
Mol Microbiol. 2014 Sep;93(6):1284-301
25069588
G3 (Bethesda). 2014 Jan 10;4(1):11-8
24192834