Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads

PLoS ONE

Volumn 9, Issue 10, 2014, Pages

  Kamada, Mayumi ^a   Hase, Sumitaka ^a   Sato, Kengo ^a   Toyoda, Atsushi ^b   Fujiyama, Asao ^b,c   Sakakibara, Yasubumi ^a  

^a KEIO UNIVERSITY   (Japan)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

^c NATIONAL INSTITUTE OF INFORMATICS   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; CYTOSINE; GUANINE;

ARTICLE; BACILLUS SUBTILIS; BACTERIAL GENOME; COMPUTER PROGRAM; DNA BASE COMPOSITION; GENE IDENTIFICATION; GENE INSERTION SEQUENCE; GENE SEQUENCE; GENETIC ANALYZER; NONHUMAN; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; BACTERIAL GENE; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; PROCEDURES;

BACILLUS SUBTILIS;

BACILLUS SUBTILIS; GENES, BACTERIAL; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING;

EID: 84908045076     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0109999     Document Type: Article

References (46)

1. Sanger F, Nicklen S, Coulson A (1977) DNA sequencing with chain-terminating inhibitors. Procedings of the National Academy of Sciences, USA 74: 5463-5467.
2. Didelot X, Bowden R, Wilson DJ, Peto TE, Crook DW (2012) Transforming clinical microbiology with bacterial genome sequencing. Nature Reviews Genetics 13: 601-612.
3. Köser CU, Ellington MJ, Cartwright EJ, Gillespie SH, Brown NM, et al. (2012) Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathogens 8: e1002824.
4. Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, et al. (2012) GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Research 22: 557-567.
5. Treangen TJ, Salzberg SL (2012) Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nature Reviews Genetics 13: 36-46.
6. Koren S, Harhay GP, Smith TPL, Bono JL, Harhay DM, et al. (2013) Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biology 14: R101.
7. Zhang X, Davenport KW, Gu W, Daligault HE, Munk AC, et al. (2012) Improving genome assemblies by sequencing PCR products with PacBio. BioTechniques 53: 61-62.
8. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, et al. (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nature Methods 10: 563-569.
9. Nishito Y, Osana Y, Hachiya T, Popendorf K, Toyoda A, et al. (2010) Whole genome assembly of a natto production strain bacillus subtilis natto from very short read data. BMC Genomics 11: 243.
10. Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, et al. (1997) The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature 390: 249-256.
11. Chin CS, Sorenson J, Harris JB, Robins WP, Charles RC, et al. (2011) The Origin of the Haitian Cholera Outbreak Strain. New England Journal of Medicine 364: 33-42.
12. Rasko DA, Webster DR, Sahl JW, Bashir A, Boisen N, et al. (2011) Origins of the E. coli Strain Causing an Outbreak of Hemolytic-Uremic Syndrome in Germany. New England Journal of Medicine 365: 709-717.
13. Glenn T (2014). 2014 NGS Field Guide: Overview. http://www.molecularecologist.com/next-gen-fieldguide-2014/. Accessed 2014 September.
14. Ribeiro FJ, Przybylski D, Yin S, Sharpe T, Gnerre S, et al. (2012) Finished bacterial genomes from shotgun sequence data. Genome Research 22: 2270-2277.
15. English AC, Richards S, Han Y, Wang M, Vee V (2012) Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology. PLoS ONE 7: e47768.
16. Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, et al. (2012) Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology 30: 693-700.
17. Au KF, Underwood JG, Lee L, Wong WH (2012) Improving PacBio Long Read Accuracy by Short Read Alignment. PLoS ONE 7: e46679.
18. ECTools website. https://github.com/jgurtowski/ectools. Accessed 2014 September.
19. Deshpande V, Fung ED, Pham S, Bafna V (2013) Cerulean: A hybrid assembly using high through-put short and long reads. Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013).
20. Single pass read accuracy improver (Sprai) website. http://zombie.cb.k.u-tokyo.ac.jp/sprai/index.html. Accessed 2014 September.
21. Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, et al. (2000) A Whole-Genome Assembly of Drosophila. Science 287: 2196-2204.
22. Itaya M, Matsui K (1999) Conversion of bacillus subtilis 168: Natto producing bacillus subtilis with Mosaic Genomes. Bioscience, Biotechnology, and Biochemistry 63: 2034-2037.
23. Chaisson MJ, Tesler G (2012) Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics 13: 238.
24. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics 25: 1754-1760.
25. Quiver website. https://github.com/PacificBiosciences/GenomicConsensus/blob/master/doc/HowToQuiver.rst. Accessed 2014 September.
26. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, et al. (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology 19: 455-477.
27. Zimin A, Marc¸ais G, Puiu D, Roberts M, Salzberg SL, et al. (2013) The MaSuRCA genome Assembler. Bioinformatics 29: 2669-2677.
28. AMOS - A Modular Open-Source Assembler website. http://amos.sourceforge.net. Accessed 2014 September.
29. Carneiro MO, Russ C, Ross MG, Gabriel SB, Nusbaum C, et al. (2012) Pacific biosciences sequencing technology for genotyping and variation discovery in human data. BMC Genomics 13: 375.
30. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al. (2010) The Genome Analysis Toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data. Genome Research 20: 1297-1303.
31. Nakamura K, Oshima T, Morimoto T, Ikeda S, Yoshikawa H, et al. (2011) Sequence-specific error profile of illumina sequencers. Nucleic Acids Research 39: e90.
32. Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J (2009) DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 25: 119-20.
33. Popendorf K, Hachiya T, Osana Y, Sakakibara Y (2010) Murasaki: A Fast, Parallelizable Algorithm to Find Anchors from Multiple Genomes. PLoS ONE 5: e12651.
34. Barbe V, Cruveiller S, Kunst F, Lenoble P, Meurice G, et al. (2009) From a consortium sequence to a unified sequence: the bacillus subtilis 168 reference genome a decade later. Microbiology 155: 1758-1775.
35. Qiu D, Fujita K, Sakuma Y, Tanaka T, Ohashi Y, et al. (2004) Comparative analysis of Physical Maps of Four Bacillus subtilis (natto) Genomes. Applied and Environmental Microbiology 70: 6247-6256.
36. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, et al. (2009) ABySS: a parallel assembler for short read sequence data. Genome Research 19: 1117-1123.
37. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, et al. (2004) Versatile and open software for comparing large genomes. Genome Biology 5: R12.
38. Lobry JR (1996) Asymmetric substitution patterns in the two DNA strands of bacteria. Molecular Biology and Evolution 13: 660-665.
39. Thorvaldsdóttir H, Robinson JT, Mesirov JP (2013) Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinformatics 14: 178-192.
40. xBASE bacterial genome annotation service website. http://www.xbase.ac.uk/annotation/. Accessed 2014 September.
41. Delcher AL, Bratke KA, Powers EC, Salzberg SL (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673-679.
42. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964.
43. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, et al. (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Research 35: 3100-3108.
44. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, et al. (2008) BLAST+: architecture and applications. BMC Bioinformatics 10: 421.
45. García-Alcalde F, Okonechnikov K, Carbonell J, Cruz LM, Götz S, et al. (2012) Qualimap: evaluating next-generation sequencing alignment data. Bioinformatics 28: 2678-2679.
46. Gurevich A, Saveliev V, Vyahhi N, Tesler G (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics 29: 1072-1075.