Insights into structural variations and genome rearrangements in prokaryotic genomes

Bioinformatics

Volumn 31, Issue 1, 2015, Pages 1-9

  Periwal, Vinita ^a,b   Scaria, Vinod ^a,b  

^a CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY   (India)

^b ACADEMY OF SCIENTIFIC AND INNOVATIVE RESEARCH ACSIR   (India)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); EUKARYOTA; PROKARYOTA;

BACTERIAL GENOME; BACTERIUM; COPY NUMBER VARIATION; DNA SEQUENCE; GENE REARRANGEMENT; GENETICS; METABOLISM; PROKARYOTIC CELL;

BACTERIA; DNA COPY NUMBER VARIATIONS; GENE REARRANGEMENT; GENOME, BACTERIAL; PROKARYOTIC CELLS; SEQUENCE ANALYSIS, DNA;

EID: 84922349709     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu600     Document Type: Review

References (98)

1. Achaz,G. et al. (2002) Origin and fate of repeats in bacteria. Nucleic Acids Res., 30, 2987-2994.
2. Alkan,C. et al. (2011) Genome structural variation discovery and genotyping. Nat. Rev. Genet., 12, 363-376.
3. Anderson,R.P. and Roth,J.R. (1977) Tandem genetic duplications in phage and bacteria. Annu. Rev. Microbiol., 31, 473-505.
4. Andersson,D.I. et al. (1998) Evidence that gene amplification underlies adaptive mutability of the bacterial lac operon. Science, 282, 1133-1135.
5. Angiuoli,S.V. and Salzberg,S.L. (2011) Mugsy: fast multiple alignment of closely related whole genomes. Bioinformatics, 27, 334-342.
6. Angov,E. and Brusilow,W.S. (1994) Effects of deletions in the uncA-uncG intergenic regions on expression of uncG, the gene for the gamma subunit of the Escherichia coli F1Fo-ATPase. Biochim. Biophys. Acta, 1183, 499-503.
7. Aras,R.A. et al. (2003) Extensive repetitive DNA facilitates prokaryotic genome plasticity. Proc. Natl Acad. Sci. USA, 100, 13579-13584.
8. Bao,Z. et al. (2014) Genomic plasticity enables phenotypic variation of Pseudomonas syringae pv. tomato DC3000. PLoS One, 9, e86628.
9. Bartenhagen,C. and Dugas,M. (2013) RSVSim: an R/Bioconductor package for the simulation of structural variations. Bioinformatics, 29, 1679-1681.
10. Beer,N.R. et al. (2007) On-chip, real-time, single-copy polymerase chain reaction in picoliter droplets. Anal. Chem., 79, 8471-8475.
11. Bentley,S.D. and Parkhill,J. (2004) Comparative genomic structure of prokaryotes. Annu. Rev. Genet., 38, 771-792.
12. Bentley,S.D. et al. (2007) Meningococcal genetic variation mechanisms viewed through comparative analysis of serogroup C strain FAM18. PLoS Genet., 3, e23.
13. Block,D.H. et al. (2012) Regulatory consequences of gene translocation in bacteria. Nucleic Acids Res., 40, 8979-8992.
14. Blount,Z.D. et al. (2012) Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature, 489, 513-518.
15. Brown,N.L. and Evans,L.R. (1991) Transposition in prokaryotes: transposon Tn501. Res. Microbiol., 142, 689-700.
16. Campo,N. et al. (2004) Chromosomal constraints in Gram-positive bacteria revealed by artificial inversions. Mol. Microbiol., 51, 511-522.
17. Carter,N.P. (2007) Methods and strategies for analyzing copy number variation using DNA microarrays. Nat. Genet., 39, S16-S21.
18. Celamkoti,S. et al. (2004) GeneOrder3.0: software for comparing the order of genes in pairs of small bacterial genomes. BMC Bioinformatics, 5, 52.
19. Chen,K. et al. (2009) BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat. Methods, 6, 677-681.
20. Chiang,D.Y. et al. (2009) High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat. Methods, 6, 99-103.
21. Chiara,M. et al. (2012) SVM(2): an improved paired-end-based tool for the detection of small genomic structural variations using high-throughput single-genome resequencing data. Nucleic Acids Res., 40, e145.
22. Chin,C.S. et al. (2013) Nonhybrid, finished microbial genome assemblies from longread SMRT sequencing data. Nat. Methods, 10, 563-569.
23. Cong,L. et al. (2013) Multiplex genome engineering using CRISPR/Cas systems. Science, 339, 819-823.
24. Cui,L. et al. (2012) Coordinated phenotype switching with large-scale chromosome flip-flop inversion observed in bacteria. Proc. Natl Acad. Sci. USA, 109, E1647-E1656.
25. Darling,A.C. et al. (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res., 14, 1394-1403.
26. Darling,A.E. et al. (2008) Dynamics of genome rearrangement in bacterial populations. PLoS Genet., 4, e1000128.
27. Das,S.K. et al. (2010) Single molecule linear analysis of DNA in nano-channel labeled with sequence specific fluorescent probes. Nucleic Acids Res., 38, e177.
28. Deurenberg,R.H. et al. (2007) The molecular evolution of methicillin-resistant Staphylococcus aureus. Clin. Microbiol. Infect., 13, 222-235.
29. Diep,B.A. et al. (2006) Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus. Lancet, 367, 731-739.
30. Dobinsky,S. et al. (2002) Influence of Tn917 insertion on transcription of the icaADBC operon in six biofilm-negative transposon mutants of Staphylococcus epidermidis. Plasmid, 47, 10-17.
31. Eisen,J.A. et al. (2000) Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biol., 1, RESEARCH0011.
32. Ellis,T. et al. (2011) DNA assembly for synthetic biology: from parts to pathways and beyond. Integr. Biol. (Camb), 3, 109-118.
33. Enyeart,P.J. et al. (2013) Generalized bacterial genome editing using mobile group II introns and Cre-lox. Mol. Syst. Biol., 9, 685.
34. Feil,E.J. et al. (2003) How clonal is Staphylococcus aureus? J. Bacteriol., 185, 3307-3316.
35. Freeman,J.L. et al. (2006) Copy number variation: new insights in genome diversity. Genome Res., 16, 949-961.
36. Freund,A.M. et al. (1989) Z-DNA-forming sequences are spontaneous deletion hot spots. Proc. Natl Acad. Sci. USA, 86, 7465-7469.
37. Fukiya,S. et al. (2004) An improved method for deleting large regions of Escherichia coli K-12 chromosome using a combination of Cre/loxP and lambda Red. FEMS Microbiol.Lett., 234, 325-331.
38. Furuta,Y. et al. (2011) Birth and death of genes linked to chromosomal inversion. Proc. Natl Acad. Sci. USA, 108, 1501-1506.
39. Gaudriault,S. et al. (2008) Plastic architecture of bacterial genome revealed by comparative genomics of Photorhabdus variants. Genome Biol., 9, R117.
40. Gommans,W.M. et al. (2005) Engineering zinc finger protein transcription factors: the therapeutic relevance of switching endogenous gene expression on or off at command. J. Mol. Biol., 354, 507-519.
41. Guijo,M.I. et al. (2001) Localized remodeling of the Escherichia coli chromosome: the patchwork of segments refractory and tolerant to inversion near the replication terminus. Genetics, 157, 1413-1423.
42. Hastings,P.J. et al. (2009a) A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet., 5, e1000327.
43. Hastings,P.J. et al. (2009b) Mechanisms of change in gene copy number. Nat. Rev. Genet., 10, 551-564.
44. Hill,C.W. and Harnish,B.W. (1981) Inversions between ribosomal RNA genes of Escherichia coli. Proc. Natl Acad. Sci. USA, 78, 7069-7072.
45. Hormozdiari,F. et al. (2009) Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res., 19, 1270-1278.
46. Hormozdiari,F. et al. (2010) Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics, 26, i350-i357.
47. Hubner,A. and Hendrickson,W. (1997) A fusion promoter created by a new insertion sequence, IS1490, activates transcription of 2,4,5-trichlorophenoxyacetic acid catabolic genes in Burkholderia cepacia AC1100. J. Bacteriol., 179, 2717-2723.
48. Huddleston,J. et al. (2014) Reconstructing complex regions of genomes using longread sequencing technology. Genome Res., 24, 688-696.
49. Hughes,D. (2000) Evaluating genome dynamics: the constraints on rearrangements within bacterial genomes. Genome Biol., 1, REVIEWS0006.
50. Iafrate,A.J. et al. (2004) Detection of large-scale variation in the human genome. Nat. Genet., 36, 949-951.
51. Jasin,M. and Schimmel,P. (1984) Deletion of an essential gene in Escherichia coli by site-specific recombination with linear DNA fragments. J. Bacteriol., 159, 783-786.
52. Jiang,Y. et al. (2012) PRISM: pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants. Bioinformatics, 28, 2576-2583.
53. Johnson,R.C. (1991) Mechanism of site-specific DNA inversion in bacteria. Curr. Opin. Genet. Dev., 1, 404-411.
54. Katapadi,V.K. et al. (2012) Potential G-quadruplex formation at breakpoint regions of chromosomal translocations in cancer may explain their fragility. Genomics, 100, 72-80.
55. Korbel,J.O. et al. (2009) PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol., 10, R23.
56. Kresse,A.U. et al. (2003) Impact of large chromosomal inversions on the adaptation and evolution of Pseudomonas aeruginosa chronically colonizing cystic fibrosis lungs. Mol. Microbiol., 47, 145-158.
57. Lee,S. et al. (2009) MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions. Nat. Methods, 6, 473-474.
58. Liang,Y. et al. (2010) Genome rearrangements of completely sequenced strains of Yersinia pestis. J. Clin. Microbiol., 48, 1619-1623.
59. Lim,K. et al. (2012) Large variations in bacterial ribosomal RNA genes. Mol. Biol. Evol., 29, 2937-2948.
60. Lu,C.L. et al. (2006) Analysis of circular genome rearrangement by fusions, fissions and block-interchanges. BMC Bioinformatics, 7, 295.
61. Mackiewicz,P. et al. (2001) Flip-flop around the origin and terminus of replication in prokaryotic genomes. Genome Biol., 2, INTERACTIONS1004.
62. Mahillon,J. and Chandler,M. (1998) Insertion sequences. Microbiol. Mol. Biol. Rev., 62, 725-774.
63. Marguet,P. et al. (2007) Biology by design: reduction and synthesis of cellular components and behaviour. J. R. Soc. Interface, 4, 607-623.
64. Marttinen,P. et al. (2012) Detection of recombination events in bacterial genomes from large population samples. Nucleic Acids Res., 40, e6.
65. Mazumder,R. et al. (2001) GeneOrder: comparing the order of genes in small genomes. Bioinformatics, 17, 162-166.
66. Medvedev,P. et al. (2009) Computational methods for discovering structural variation with next-generation sequencing. Nat. Methods, 6, S13-S20.
67. Miesel,L. et al. (1994) Construction of chromosomal rearrangements in Salmonella by transduction: inversions of non-permissive segments are not lethal. Genetics, 137, 919-932.
68. Miller,J.C. et al. (2011) A TALE nuclease architecture for efficient genome editing. Nat. Biotechnol., 29, 143-148.
69. Morrow,J.D. and Cooper,V.S. (2012) Evolutionary effects of translocations in bacterial genomes. Genome Biol. Evol., 4, 1256-1262.
70. Naas,T. et al. (1995) Dynamics of IS-related genetic rearrangements in resting Escherichia coli K-12. Mol. Biol. Evol., 12, 198-207.
71. Nagarajan,S. et al. (2012) Functions of the duplicated hik31 operons in central metabolism and responses to light, dark, and carbon sources in Synechocystis sp. strain PCC 6803. J. Bacteriol., 194, 448-459.
72. Nelson,K.E. et al. (1999) Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritime. Nature, 399, 323-329.
73. Nogami,T. et al. (1985) Construction of a series of ompF-ompC chimeric genes by in vivo homologous recombination in Escherichia coli and characterization of the translational products. J. Bacteriol., 164, 797-801.
74. Ochman,H. et al. (2000) Lateral gene transfer and the nature of bacterial innovation. Nature, 405, 299-304.
75. Okinaka,R.T. et al. (2011) An attenuated strain of Bacillus anthracis (CDC 684) has a large chromosomal inversion and altered growth kinetics. BMC Genomics, 12, 477.
76. Oliver,A. et al. (2002) The mismatch repair system (mutS, mutL and uvrD genes) in Pseudomonas aeruginosa: molecular characterization of naturally occurring mutants. Mol. Microbiol., 43, 1641-1650.
77. Quail,M.A. et al. (2012) A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics, 13, 341.
78. Rasko,D.A. et al. (2011) Origins of the E. coli strain causing an outbreak of hemolytic- uremic syndrome in Germany. N. Engl. J. Med., 365, 709-717.
79. Rausch,T. et al. (2012) DELLY: structural variant discovery by integrated pairedend and split-read analysis. Bioinformatics, 28, i333-i339.
80. Reams,A.B. and Neidle,E.L. (2004) Selection for gene clustering by tandem duplication. Annu. Rev. Microbiol., 58, 119-142.
81. Rebollo,J.E. et al. (1988) Detection and possible role of two large nondivisible zones on the Escherichia coli chromosome. Proc. Natl Acad. Sci. USA, 85, 9391-9395.
82. Rocha,E.P. (2008) The organization of the bacterial genome. Annu. Rev. Genet., 42, 211-233.
83. Roth,J. et al. (1996) Rearrangements of the bacterial chromosome: formation and applications. In: Neidhardt,F.C. (ed.) Escherichia coli and Salmonella: Cellular and Molecular Biology. ASM Press, Washington, DC, pp. 2256-2276.
84. Segall,A. et al. (1988) Rearrangement of the bacterial chromosome: forbidden inversions. Science, 241, 1314-1318.
85. Sindi,S. et al. (2009) A geometric approach for classification and comparison of structural variants. Bioinformatics, 25, i222-i230.
86. Skovgaard,O. et al. (2011) Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing. Genome Res., 21, 1388-1393.
87. Spencer-Smith,R. et al. (2012) Sequence features contributing to chromosomal rearrangements in Neisseria gonorrhoeae. PLoS One, 7, e46023.
88. Srivatsan,A. et al. (2008) High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies. PLoS Genet., 4, e1000139.
89. Sun,S. et al. (2012) Genome-wide detection of spontaneous chromosomal rearrangements in bacteria. PLoS One, 7, e42639.
90. Tatusova,T. et al. (2014) RefSeq microbial genomes database: new representation and annotation strategy. Nucleic Acids Res., 42, D553-D559.
91. Teague,B. et al. (2010) High-resolution human genome structure by single-molecule analysis. Proc. Natl Acad. Sci. USA, 107, 10848-10853.
92. Treangen,T.J. et al. (2009) Genesis, effects and fates of repeats in prokaryotic genomes. FEMS Microbiol. Rev., 33, 539-571.
93. Wang,E.A. et al. (1982) Tandem duplication and multiple functions of a receptor gene in bacterial chemotaxis. J. Biol. Chem., 257, 4673-4676.
94. Weischenfeldt,J. et al. (2013) Phenotypic impact of genomic structural variation: insights from and for human disease. Nat. Rev. Genet., 14, 125-138.
95. Wu,T.H. and Marinus,M.G. (1999) Deletion mutation analysis of the mutS gene in Escherichia coli. J. Biol. Chem., 274, 5948-5952.
96. Xing,J. et al. (2009) Mobile elements create structural variation: analysis of a complete human genome. Genome Res., 19, 1516-1526.
97. Ye,K. et al. (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics, 25, 2865-2871.
98. Zeitouni,B. et al. (2010) SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data. Bioinformatics, 26, 1895-1896.