De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads

PLoS ONE

Volumn 5, Issue 6, 2010, Pages

  Nagarajan, Harish ^a,b   Butler, Jessica E ^c   Klimes, Anna ^c,e   Qiu, Yu ^b   Zengler, Karsten ^b   Ward, Joy ^c   Young, Nelson D ^c   Methé, Barbara A ^d   Palsson, Bernhard O ^b   Lovley, Derek R ^c   Barrett, Christian L ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^c UNIVERSITY OF MASSACHUSETTS   (United States)

^d J CRAIG VENTER INSTITUTE   (United States)

^e WESTERN NEW ENGLAND UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; BACTERIAL GENOME; COMPUTER PROGRAM; CONTROLLED STUDY; DNA SEQUENCE; ELECTRIC CURRENT; GENOME ANALYSIS; GEOBACTER SULFURREDUCENS; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PREDICTION;

ALGORITHMS; ELECTRICITY; GENOME, BACTERIAL; GEOBACTER; POLYMERASE CHAIN REACTION;

GEOBACTER; GEOBACTER SULFURREDUCENS;

EID: 77956203114     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0010922     Document Type: Article

References (23)

1. Chaisson MJ, Pevzner PA (2008) Short read fragment assembly of bacterial genomes. Genome Research 18: 324-330.
2. Zerbino DR, Birney E (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18: 821-829.
3. Jeck WR, Reinhardt JA, Baltrus DA, Hickenbotham MT, Magrini V, et al. (2007) Extending assembly of short DNA sequences to handle error. Bioinformatics 23: 2942-2944.
4. Hernandez D, François P, Farinelli L, Østerås M, Schrenzel J (2008) De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer. Genome Research 18: 802-809.
5. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, et al. (2008) ALLPATHS: De novo assembly of whole-genome shotgun microreads. Genome Research 18: 810-820.
6. Reinhardt JA, Baltrus DA, Nishimura MT, Jeck WR, Jones CD, et al. (2009) De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Research 19: 294-305.
7. Aury JM, Cruaud C, Barbe V, Rogier O, Mangenot S, et al. (2008) High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies. BMC Genomics 9: 603.
8. Salzberg SL, Sommer DD, Puiu D, Lee VT (2008) Gene-boosted assembly of a novel bacterial genome from very short reads. PLoS Comput Biol 4: e1000186.
9. Croucher NJ (2009) From small reads do mighty genomes grow. Nat Rev Micro 7: 621-621.
10. Yi H, Nevin KP, Kim BC, Franks AE, Klimes A, et al. (2009) Selection of a variant of geobacter sulfurreducens with enhanced capacity for current production in microbial fuel cells. Biosensors and Bioelectronics 24: 3498-3503.
11. Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 25: 3389-3402.
12. Zhang Z, Schwartz S, Wagner L, Miller W (2000) A greedy algorithm for aligning dna sequences. Journal of Computational Biology 7: 203-214.
13. Aziz R, Bartels D, Best A, DeJongh M, Disz T, et al. (2008) The rast server: Rapid annotations using subsystems technology. BMC Genomics 9: 75.
14. Methe BA, Nelson KE, Eisen JA, Paulsen IT, Nelson W, et al. (2003) Genome of Geobacter sulfurreducens: Metal Reduction in Subsurface Environments. Science 302: 1967-1969.
15. Mahadevan R, Bond DR, Butler JE, Esteve-Nunez A, Coppi MV, et al. (2006) Characterization of Metabolism in the Fe(III)-Reducing Organism Geobacter sulfurreducens by Constraint-Based Modeling. Appl Environ Microbiol 72: 1558-1568.
16. Pruitt KD, Tatusova T, Klimke W, Maglott DR (2009) NCBI Reference Sequences: current status, policy and new initiatives. Nucl Acids Res 37: D32-36.
17. Lovley DR (2008) The microbe electric: conversion of organic matter to electricity. Current Opinion in Biotechnology 19: 564-571.
18. Mehta T, Coppi MV, Childers SE, Lovley DR (2005) Outer Membrane c-Type Cytochromes Required for Fe(III) and Mn(IV) Oxide Reduction in Geobacter sulfurreducens. Appl Environ Microbiol 71: 8634-8641.
19. Aziz RK, Breitbart M, Edwards RA (2010) Transposases are the most abundant, most ubiquitous genes in nature. Nucl Acids Res gkq 140.
20. Chaisson MJ, Brinza D, Pevzner PA (2009) De novo fragment assembly with short mate-paired reads: Does the read length matter? Genome Research 19: 336-346.
21. Delcher AL, Phillippy A, Carlton J, Salzberg SL (2002) Fast algorithms for large-scale genome alignment and comparison. Nucl Acids Res 30: 2478-2483.
22. Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, et al. (2000) Comparative Genomics of the Eukaryotes. Science 287: 2204-2215.
23. Pearson W, Lipman D (1995) Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences 85: 2444-2448.