Efficient de novo assembly of single-cell bacterial genomes from short-read data sets

Nature Biotechnology

Volumn 29, Issue 10, 2011, Pages 915-922

  Chitsaz, Hamidreza ^a   Yee Greenbaum, Joyclyn L ^b   Tesler, Glenn ^a   Lombardo, Mary Jane ^b   Dupont, Christopher L ^b   Badger, Jonathan H ^b   Novotny, Mark ^b   Rusch, Douglas B ^b   Fraser, Louise J ^c   Gormley, Niall A ^c   Schulz Trieglaff, Ole ^c   Smith, Geoffrey P ^c   Evers, Dirk J ^b   Pevzner, Pavel A ^a   Lasken, Roger S ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b J CRAIG VENTER INSTITUTE   (United States)

^c ILLUMINA INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GENOMES; BACTERIAL LINEAGES; CONTIGS; DATA SETS; E. COLI; GENETIC INFORMATION; GENOME ASSEMBLY; GLOBAL OCEAN; METABOLIC RECONSTRUCTION; MULTIPLE DISPLACEMENT AMPLIFICATIONS; SINGLE CELLS; STAPHYLOCOCCUS AUREUS; UNCULTIVATED BACTERIA; WHOLE GENOME AMPLIFICATIONS;

BACTERIA; BACTERIOLOGY; ESCHERICHIA COLI; GENE ENCODING;

CELLS;

BACTERIAL DNA; CONTIG; RIBOSOME RNA; TRANSFER RNA;

ARTICLE; BACTERIAL CELL; BACTERIAL GENOME; DELTAPROTEOBACTERIA; DNA SEQUENCE; ESCHERICHIA COLI; GENE AMPLIFICATION; MAXIMUM LIKELIHOOD METHOD; MULTIPLE DISPLACEMENT AMPLIFICATION; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; STAPHYLOCOCCUS AUREUS;

ALGORITHMS; BACTERIA; BASE SEQUENCE; CONTIG MAPPING; DATABASES, NUCLEIC ACID; DELTAPROTEOBACTERIA; ESCHERICHIA COLI; GENOME, BACTERIAL; LIKELIHOOD FUNCTIONS; SEQUENCE ANALYSIS, DNA; SINGLE-CELL ANALYSIS; STAPHYLOCOCCUS AUREUS;

BACTERIA (MICROORGANISMS); DELTAPROTEOBACTERIA; ESCHERICHIA COLI; STAPHYLOCOCCUS AUREUS;

EID: 80054732674     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.1966     Document Type: Article

References (47)

1. Rusch, D.B. et al. The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through eastern tropical Pacific. PLoS Biol. 5, e77 (2007
2. Gill, S.R. et al. Metagenomic analysis of the human distal gut microbiome. Science 312, 1355-1359 (2006 (Pubitemid 43839542)
3. Raghunathan, A. et al. Genomic DNA amplification from a single bacterium. Appl. Environ. Microbiol. 71, 3342-3347 (2005 (Pubitemid 40807247)
4. Dean, F.B. et al. Comprehensive human genome amplification using multiple displacement amplification. Proc. Natl. Acad. Sci. USA 99, 5261-5266 (2002 (Pubitemid 34411536)
5. Dean, F.B., Nelson, J.R., Giesler, T.L. & Lasken, R.S. Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res. 11, 1095-1099 (2001 (Pubitemid 32834553)
6. Hosono, S. et al. Unbiased whole-genome amplification directly from clinical samples. Genome Res. 13, 954-964 (2003 (Pubitemid 36621755)
7. Lasken, R.S. Single cell genomic sequencing using Multiple Displacement Amplification. Curr. Opin. Microbiol. 10, 510-516 (2007 (Pubitemid 350052686)
8. Ishoey, T., Woyke, T., Stepanauskas, R., Novotny, M. & Lasken, R.S. Genomic sequencing of single microbial cells from environmental samples. Curr. Opin. Microbiol. 11, 198-204 (2008
9. Zhang, K. et al. Sequencing genomes from single cells by polymerase cloning. Nat. Biotechnol. 24, 680-686 (2006 (Pubitemid 43882119)
10. Lasken, R.S. & Stockwell, T.B. Mechanism of chimera formation during the Multiple Displacement Amplification reaction. BMC Biotechnol. 7, 19 (2007
11. Lasken, R.S. et al. Multiple displacement amplification from single bacterial cells in Whole Genome Amplification: Methods Express (eds. Hughes, S. & Lasken, R.) 119-147 (Scion Publishing Ltd., UK, 2005
12. Kvist, T., Ahring, B.K., Lasken, R.S. & Westermann, P. Specific single-cell isolation and genomic amplification of uncultured microorganisms. Appl. Microbiol. Biotechnol. 74, 926-935 (2007
13. Mussmann, M. et al. Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. PLoS Biol. 5, e230 (2007
14. Marcy, Y. et al. Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc. Natl. Acad. Sci. USA 104, 11889-11894 (2007 (Pubitemid 47185600)
15. Podar, M. et al. Targeted access to the genomes of low abundance organisms in complex microbial communities. Appl. Environ. Microbiol. 73, 3205-3214 (2007 (Pubitemid 46834971)
16. Hongoh, Y. et al. Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell. Proc. Natl. Acad. Sci. USA 105, 5555-5560 (2008 (Pubitemid 351753901)
17. Rodrigue, S. et al. Whole genome amplification and de novo assembly of single bacterial cells. PLoS ONE 4, e6864 (2009
18. Woyke, T. et al. Assembling the marine metagenome, one cell at a time. PLoS ONE 4, e5299 (2009
19. Zerbino, D.R. & Birney, E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821-829 (2008 (Pubitemid 351645072)
20. Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-380 (2005 (Pubitemid 41613494)
21. 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 (Pubitemid 32769375)
22. Simpson, J.T. et al. ABySS: A parallel assembler for short read sequence data. Genome Res. 19, 1117-1123 (2009
23. Chaisson, M.J. & Pevzner, P.A. Short read fragment assembly of bacterial genomes. Genome Res. 18, 324-330 (2008 (Pubitemid 351240742)
24. Diep, B.A. et al. Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus. Lancet 367, 731-739 (2006 (Pubitemid 43326291)
25. Wright, T.D., Vergin, K.L., Boyd, P.W. & Giovannoni, S.J. A novel delta-subdivision proteobacterial lineage from the lower ocean surface layer. Appl. Environ. Microbiol. 63, 1441-1448 (1997 (Pubitemid 27174852)
26. Noguchi, H., Park, J. & Takagi, T. MetaGene: Prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Res. 34, 5623-5630 (2006 (Pubitemid 44742449)
27. Tatusov, R.L. et al. The COG database: An updated version includes eukaryotes. BMC Bioinformatics 4, 41 (2003
28. Goldman, B.S. et al. Evolution of sensory complexity recorded in a myxobacterial genome. Proc. Natl. Acad. Sci. USA 103, 15200-15205 (2006 (Pubitemid 44583188)
29. DeLong, E.F. et al. Community genomics among stratified microbial assemblages in the ocean's interior. Science 311, 496-503 (2006 (Pubitemid 43157723)
30. Rich, V.I., Pham, V.D., Eppley, J., Shi, Y. & Delong, E.F. Time-series analyses of Monterey Bay coastal microbial picoplankton using a 'genome proxy' microarray. Environ. Microbiol. 13, 116-134 (2010
31. Yooseph, S. et al. Genomic and functional adaptation in surface ocean planktonic prokaryotes. Nature 468, 60-66 (2010
32. Iizuka, T. et al. Plesiocystis pacifica gen. nov., sp. nov., a marine myxobacterium that contains dihydrogenated menaquinone, isolated from the Pacific coasts of Japan. Int. J. Syst. Evol. Microbiol. 53, 189-195 (2003 (Pubitemid 36285239)
33. Callister, S.J. et al. Comparative bacterial proteomics: Analysis of the core genome concept. PLoS ONE 3, e1542 (2008
34. Mitreva, M. Bacterial core gene set. http://www.hmpdacc.org/doc/sops/ reference-genomes/metrics/Bacterial-CoreGenes-SOP.pdf (2008
35. Nelson, K.E. et al. A catalog of reference genomes from the human microbiome. Science 328, 994-999 (2010
36. Woyke, T. et al. One bacterial cell, one complete genome. PLoS ONE 5, e10314 (2010
37. King, G.M. Microbial carbon monoxide consumption in salt marsh sediments. FEMS Microbiol. Ecol. 59, 2-9 (2007 (Pubitemid 44952404)
38. Schloss, P.D. et al. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537-7541 (2009
39. Wilgenbusch, J.C. & Swofford, D. Inferring evolutionary trees with PAUP. Curr. Prot. Bioinformatics, Unit 6.4 6.4.1-6.4.28 (2003
40. Hernandez, D., Francois, P., Farinelli, L., Ostera, M. & Schrenzel, J. De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer. Genome Res. 18, 802-809 (2008 (Pubitemid 351645070)
41. Li, R. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265-272 (2010
42. Mao, F., Dam, P., Chou, J., Olman, V. & Xu, Y. DOOR: A database for prokaryotic operons. Nucleic Acids Res. 37, D459-D463 (2009
43. Bentley, D.R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53-59 (2008
44. Tanenbaum, D.M. et al. The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data. Stand. Genomic Sci. 2, 229-237 (2010
45. Ramirez-Flandes, S. & Ulloa, O. Bosque: Integrated phylogenetic analysis software. Bioinformatics 24, 2539-2541 (2008
46. Kanehisa, M. & Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27-30 (2000 (Pubitemid 30047706)
47. Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A.C. & Kanehisa, M. KAAS: An automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35, W182-185 (2007).