Application of 'next-generation' sequencing technologies to microbial genetics

Nature Reviews Microbiology

Volumn 7, Issue 4, 2009, Pages 287-296

  MacLean, Daniel ^a   Jones, Jonathan D G ^a   Studholme, David J ^a  

^a SAINSBURY LABORATORY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE; SHORT HAIRPIN RNA; SINGLE STRANDED DNA; BACTERIAL DNA;

BACTERIUM IDENTIFICATION; DATA ANALYSIS SOFTWARE; DNA SEQUENCE; DNA TEMPLATE; DOWNSTREAM PROCESSING; ENZYME IMMOBILIZATION; EXPRESSED SEQUENCE TAG; GENE AMPLIFICATION; GENE SEQUENCE; GENE TECHNOLOGY; GENETIC ALGORITHM; GENETIC EPIGENESIS; HIGH THROUGHPUT SCREENING; MICROBIAL GENETICS; MICROBIOLOGY; NONHUMAN; PERFORMANCE MEASUREMENT SYSTEM; PRIORITY JOURNAL; PROCESS TECHNOLOGY; PYROSEQUENCING; REVIEW; RNA ANALYSIS; SEQUENCE ANALYSIS; SEQUENCE DATABASE; STRUCTURAL BIOINFORMATICS; VIRUS EXAMINATION; BACTERIAL GENOME; BACTERIUM; BIOLOGY; GENETIC DATABASE; GENETICS; METHODOLOGY;

BACTERIA; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA, BACTERIAL; GENOME, BACTERIAL; SEQUENCE ANALYSIS, DNA;

EID: 63249121217     PISSN: 17401526     EISSN: None     Source Type: Journal    
DOI: 10.1038/nrmicro2088     Document Type: Review

References (75)

1. Pop, M. & Salzberg, S. L. Bioinformatics challenges of new sequencing technology. Trends Genet. 24, 142-149 (2008).
2. Trombetti, G. A., Bonnal, R. J., Rizzi, E., De Bellis, G. & Milanesi, L. Data handling strategies for high throughput pyrosequencers. BMC Bioinformatics 8, S22 (2007).
3. Hall, N. Advanced sequencing technologies and their wider impact in microbiology. J. Exp. Biol. 210, 1518-1525 (2007).
4. Holt, R. A. & Jones, S. J. The new paradigm of flow cell sequencing. Genome Res. 18, 839-846 (2008).
5. Mardis, E. R. The impact of next-generation sequencing technology on genetics. Trends Genet. 24, 133-141 (2008).
6. Mardis, E. R. Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet. 9, 387-402 (2008).
7. Marguerat, S., Wilhelm, B. T. & Bähler, J. Next-generation sequencing: Applications beyond genomes. Biochem. Soc. Trans. 36, 1091-1096 (2008).
8. Medini, D. et al. Microbiology in the post-genomic era. Nature Rev. Microbiol. 6, 419-430 (2008).
9. Rusk, N. & Kiermer, V. Primer: Sequencing - the next generation. Nature Methods 5, 15 (2008).
10. Schuster, S. C. Next-generation sequencing transforms today's biology. Nature Methods 5, 16-18 (2008).
11. Shendure, J. & Ji, H. Next-generation DNA sequencing. Nature Biotechnol. 26, 1135-1145 (2008).
12. Snyder, L. A., Loman, N., Pallen, M. J. & Penn, C. W. Next-generation sequencing - the promise and perils of charting the great microbial unknown. Microb. Ecol. 57, 1-3 (2009).
13. Steinberg, K. M., Okou, D. T. & Zwick, M. E. Applying rapid genome sequencing technologies to characterize pathogen genomes. Anal. Chem. 80, 520-528 (2008).
14. Wold, B. & Myers, R. M. Sequence census methods functional genomics. Nature Methods 5, 19-21 (2008).
15. Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-380 (2005).
16. Braslavsky, I., Hebert, B., Kartalov, E. & Quake, S, R. Sequence information can be obtained from single DNA molecules. Proc. Natl Acad. Sci. USA 100, 3960-3964 (2003).
17. Harris, T. D. et al. Single-molecule DNA sequencing a viral genome. Science 320, 106-109 (2008).
18. Medini, D., Donati, C., Tettelin, H., Masignani, V. & Rappuoli, R. The microbial pan-genome. Curr. Opin. Genet. Dev. 15, 589-594 (2005).
19. Velicer, G. J. Comprehensive mutation identification an evolved bacterial cooperator and its cheating ancestor. Proc. Natl Acad. Sci. USA 103, 8107-8112 (2006).
20. Mardis, E., McPherson, J., Martienssen, R., Wilson, R. K. & McCombie, W. R. What is finished, and why does it matter. Genome Res. 12, 669-671 (2002).
21. Stiens, M. et al. Comparative genomic hybridisation and ultrafast pyrosequencing revealed remarkable differences between the Sinorhizobium meliloti genomes of the model strain Rm1021 and the field isolate SM11. J. Biotechnol. 136, 31-37 (2008).
22. La Scola, B. et al. Rapid comparative genomic analysis for clinical microbiology: The Francisella tularensis paradigm. Genome Res. 18, 742-750 (2008).
23. Dinsdale, E. A. et al. Functional metagenomic profiling of nine biomes. Nature 455, 830 (2008).
24. Ossowski, S. et al. Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res. 18, 2024-2033 (2008).
25. Baird, N. A. et al. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3, e3376 (2008).
26. Holt, K. E. et al. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nature Genet. 40, 987-993 (2008).
27. Liu, Z. et al. Patterns of diversifying selection in the phytotoxin-like scr74 gene family of Phytophthora infestans. Mol. Biol. Evol. 22, 659-672 (2004).
28. Kamoun, S. A catalogue of the effector secretome of plant pathogenic oomycetes. Annu. Rev. Phytopathol. 44, 41-60 (2006).
29. Srivatsan, A. et al. High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies. PLoS Genet. 4 e1000139 (2008).
30. Loman, N. J. & Pallen, M. J. XDR-TB genome sequencing: A glimpse of the microbiology of the future. Future Microbiol. 3, 111-113 (2008).
31. Velculescu, V. E., Zhang, L., Vogelstein, B. & Kinzler, K. W. Serial analysis of gene expression. Science 270, 484-487 (1995).
32. Cheung, F. et al. Analysis of the Pythium ultimum transcriptome using Sanger and pyrosequencing approaches. BMC Genomics 9, 542 (2008).
33. Cloonan, N. et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nature Methods 5, 613-619 (2008).
34. Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 5, 621-628 (2008).
35. Nagalakshmi, U. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344-1349 (2008).
36. Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523-536 (2008).
37. Marioni, J. C., Mason, C. E., Mane, S. M., Stephens, M. & Gilad, Y. RNA-Seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 18, 1509-1517 (2008).
38. Shendure, J. The beginning of the end for microarrays? Nature Methods 5, 585-587 (2008).
39. Ren, B. et al. Genome-wide location and function of DNA binding proteins. Science 290, 2306-2309 (2000).
40. Johnson, D. S., Mortazavi, A., Myers, R. M. & Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science 316 1497-1502 (2007).
41. Taylor, K. H. Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Res. 67, 8511-8518 (2007).
42. Cokus, S. J. et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215-219 (2008).
43. Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823-837 (2007).
44. Hakimi, M. A. & Deitsch, K. W. Epigenetics in Apicomplexa: Control of gene expression during cell cycle progression, differentiation and antigenic variation. Curr. Opin. Microbiol. 10, 357-362 (2007).
45. Wang, G. P., Ciuffi, A., Leipzig, J., Berry, C. C. & Bushman, F. D. HIV integration site selection: Analysis by massively parallel pyrosequencing reveals association with epigenetic modifications. Genome Res. 17, 1186-1194 (2007).
46. Molnár, A., Schwach, F., Studholme, D. J., Thuenemann, E. C. & Baulcombe, D. C. miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature 447, 1126-1129 (2007).
47. Dohm, J. C., Lottaz, C., Borodina, T. & Himmelbauer, H. SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Res. 17, 1697-1706 (2007).
48. Warren, R. L., Sutton, G. G., Jones, S. J. & Holt, R. A. Assembling millions of short DNA sequences using SSAKE. Bioinformatics 23 500-501 (2007).
49. Jeck, W. R. et al. Extending assembly of short DNA sequences to handle error. Bioinformatics 23, 2942-2944 (2007).
50. Pevzner, P. A., Tang, H. & Waterman, M. S. An Eulerian path approach to DNA fragment assembly. Proc. Natl Acad. Sci. USA 98, 9748-9753 (2001).
51. Zerbino, D. R. & Birney, E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821-829 (2008).
52. Chaisson, M. J. & Pevzner, P. A. Short read fragment assembly of bacterial genomes. Genome Res. 18, 324-330 (2008).
53. Hernandez, D., François, P., Farinelli, L., Osterås, M. & Schrenzel, J. De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer. Genome Res. 18, 802-809 (2008).
54. Butler, J. et al. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res. 18, 810-820 (2008).
55. Phillippy, A. M., Schatz, M. C. & Pop, M. Genome assembly forensics: finding the elusive mis-assembly. Genome Biol. 9, R55 (2008).
56. Huang, W. & Marth, G. EagleView: A genome assembly viewer for next-generation sequencing technologies. Genome Res. 18, 1538-1543 (2008).
57. Farrer, R. A., Kemen, E., Jones, J. D. G. & Studholme, D. J. De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads. FEMS Microbiol. Lett. 291, 103-111 (2009).
58. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403-410 (1990).
59. Kent, W. J. BLAT - the BLAST-like alignment tool. Genome Res. 12, 656-664 (2002).
60. Ning, Z., Cox, A. J. & Mullikin, J. C. SSAHA: A fast search method for large DNA databases. Genome Res. 11, 1725-1729 (2001).
61. Li, H., Ruan, J. & Durbin, R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18 1851-1858 (2008).
62. Wu, T. D. & Watanabe, C. K. GMAP: A genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21, 1859-1875 (2005).
63. Smith, A. D., Xuan, Z. & Zhang, M. Q. Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics 9, 128 (2008).
64. Prüfer, K. et al. PatMaN: Rapid alignment of short sequences to large databases. Bioinformatics 24, 1530-1531 (2008).
65. Li, R., Li, Y., Kristiansen, K. & Wang, J. SOAP: Short oligonucleotide alignment program. Bioinformatics 24, 713-714 (2008).
66. Jiang, H. & Wong, W. H. SeqMap: Mapping massive amount of oligonucleotides to the genome. Bioinformatics 24, 2395-2396 (2008).
67. Coarfa, C. & Milosavljevic, A. Pash 2.0: Scaleable sequence anchoring for next-generation sequencing technologies. Pac. Symp. Biocomput. 102-113 (2008).
68. Fejes, A. P. et al. FindPeaks 3.1: A tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 24, 1729-1730 (2008).
69. Valouev, A. et al. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nature Methods 5, 829-834 (2008).
70. Stein, L. D. The generic genome browser: A building block for a model organism system database. Genome Res. 12, 1599-1610 (2002).
71. Barton, G. et al. EMAAS: An extensible grid-based rich internet application for microarray data analysis and management. BMC Bioinformatics 9, 493 (2008).
72. Huntley, D., Tang, Y. A., Nesterova, T. B., Butcher, S. & Brockdorff, N. Genome Environment Browser (GEB): A dynamic browser for visualising high-throughput experimental data in the context of genome features. BMC Bioinformatics 9, 501 (2008).
73. Field, D. et al. The minimum information about a genome sequence (MIGS) specification. Nature Biotechnol. 26, 541-547 (2008).
74. Aury, J. M. High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies. BMC Genomics 9, 603 (2008).
75. Reinhardt, J. A. et al. De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Res. 19, 294-305 (2009).