Efficient and accurate whole genome assembly and methylome profiling of E. coli

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Powers, Jason G ^a   Weigman, Victor J ^a   Shu, Jenny ^a   Pufky, John M ^a   Cox, Donald ^a   Hurban, Patrick ^a  

^a IQVIA   (United States)

Author keywords

5mC; Base modifications; E. coli; Genome assembly; Hybrid assembly; Illumina MiSeq; Ion Torrent PGM; PacBio RS

Indexed keywords

DNA (CYTOSINE 5) METHYLTRANSFERASE; DNA ADENINE METHYLTRANSFERASE;

ACCURACY; ARTICLE; AUTOANALYZER; BACTERIAL GENOME; BACTERIAL STRAIN; BIOINFORMATICS; CONTROLLED STUDY; DNA LIBRARY; DNA METHYLATION; DNA MODIFICATION; ESCHERICHIA COLI; GENOME ANALYSIS; GENOTYPE; HYBRID; INTERMETHOD COMPARISON; METHYLOME PROFILING; NONHUMAN; NUCLEOTIDE SEQUENCE; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; DNA SEQUENCE; GENETICS;

BACTERIA (MICROORGANISMS);

BASE SEQUENCE; DNA METHYLATION; ESCHERICHIA COLI; GENOME, BACTERIAL; SEQUENCE ANALYSIS, DNA;

EID: 84884854581     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-675     Document Type: Article

References (48)

1. Whitman WB, Coleman DC, Wiebe WJ. Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A 1998, 95(12):6578-6583. 10.1073/pnas.95.12.6578, 33863, 9618454.
2. Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, Hoon J, Simons JF, Marran D, Myers JW, Davidson JF, Branting A, Nobile JR, Puc BP, Light D, Clark TA, Huber M, Branciforte JT, Stoner IB, Cawley SE, Lyons M, Fu Y, Homer N, Sedova M, Miao X, Reed B, et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011, 475(7356):348-352. 10.1038/nature10242, 21776081.
3. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008, 456(7218):53-59. 10.1038/nature07517, 2581791,2581791, 18987734.
4. Zhang W, Chen J, Yang Y, Tang Y, Shang J, Shen B. A practical comparison of De novo genome assembly software tools for next-generation sequencing technologies. PLOS One 2011, 6(3). e17915.
5. Paszkiewicz K, Studholme DJ. De novo assembly of short sequence reads. Brief Bioinform 2010, 11(5):457-472. 10.1093/bib/bbq020, 20724458.
6. Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S, Dalal R, Dewinter A, Dixon J, Foquet M, Gaertner A, Hardenbol P, Heiner C, Hester K, Holden D, Kearns G, Kong X, Kuse R, Lacroix Y, Lin S, et al. Real-time DNA sequencing from single polymerase molecules. Science 2009, 323(5910):133-138. 10.1126/science.1162986, 19023044.
7. Flusberg BA, Webster DR, Lee JH, Travers KJ, Olivares EC, Clark TA, Korlach J, Turner SW. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods 2010, 7(6):461-465. 10.1038/nmeth.1459, 2879396, 20453866.
8. Fang G, Munera D, Friedman DI, Mandlik A, Chao MC, Banerjee O, Feng Z, Losic B, Mahajan MC, Jabado OJ, Deikus G, Clark TA, Luong K, Murray IA, Davis BM, Keren-Paz A, Chess A, Roberts RJ, Korlach J, Turner SW, Kumar V, Waldor MK, Schadt EE. Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nat Biotechnol 2012, 30(12):1232-1239. 10.1038/nbt.2432, 23138224.
9. Murray IA, Clark TA, Morgan RD, Boitano M, Anton BP, Luong K, Fomenkov A, Turner SW, Korlach J, Roberts RJ. The methylomes of six bacteria. Nucleic Acids Res 2012, 40(22):11450-11462. 10.1093/nar/gks891, 3526280, 23034806.
10. Saletore Y, Meyer K, Korlach J, Vilfan ID, Jaffrey S, Mason CE. The birth of the epitranscriptome: deciphering the function of RNA modifications. Genome Biol 2012, 13(10):175. 10.1186/gb-2012-13-10-175, 23113984.
11. Vilfan ID, Tsai YC, Clark TA, Wegener J, Dai Q, Yi C, Pan T, Turner SW, Korlach J. Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription. J Nanobiotechnol 2013, 11(8).
12. Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, Phillippy AM. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol 2012, 30(7):693-700. 10.1038/nbt.2280, 3707490, 22750884.
13. Au KF, Underwood JG, Lee L, Wong WH. Improving PacBio long read accuracy by short read alignment. PLOS One 2012, 7(10). e46679.
14. Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G. Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 2008, 24(24):2818-2824. 10.1093/bioinformatics/btn548, 2639302, 18952627.
15. Pacific Biosciences, Inc DevNet: SMRT® Analysis http://pacificbiosciences.github.io/DevNet/code.html, Pacific Biosciences, Inc.
16. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013, 10:563-569. 10.1038/nmeth.2474, 23644548.
17. Koren S, Harhay GP, Smith TP, Bono JL, Harhay DM, McVey SD, Radune D, Bergman NH, Phillippy AM. Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biol 2013, 14(9). R101.
18. Mavromatis K, Land ML, Brettin TS, Quest DJ, Copeland A, Clum A, Goodwin L, Woyke T, Lapidus A, Klenk HP, Cottingham RW, Kyrpides NC. The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotations. PLOS One 2012, 7(12). e48837.
19. English AC, Richards S, Han Y, Wang M, Vee V, Qu J, Qin X, Muzny DM, Reid JG, Worley KC, Gibbs RA. Mind the Gap: upgrading genomes with pacific biosciences RS long-read sequencing technology. PLOS One 2012, 7(11). e47768.
20. Daegelen P, Studier FW, Lenski RE, Cure S, Kim JF. Tracing ancestors and relatives of Escherichia coli B, and the derivation of B strains REL606 and BL21(DE3). J Mol Biol 2009, 394(3):634-643.
21. Jeong H, Barbe V, Lee CH, Vallenet D, Yu DS, Choi SH, Couloux A, Lee SW, Yoon SH, Cattolico L, Hur CG, Park HS, Ségurens B, Kim SC, Oh TK, Lenski RE, Studier FW, Daegelen P, Kim JF. Genome sequences of Escherichia coli B strains REL606 and BL21(DE3). J Mol Biol 2009, 394(4):644-652. 10.1016/j.jmb.2009.09.052, 19786035.
22. Hanahan D. Studies on transformation of Escherichia coli with plasmids. J Mol Biol 1983, 166:557-580. 10.1016/S0022-2836(83)80284-8, 6345791.
23. Marinus MG, Morris NR. Isolation of deoxyribonucleic acid methylase mutants of Escherichia coli K-12. J Bacteriol 1973, 114(3):1143-1150. 285375, 4576399.
24. Bigger CH, Murray K, Murray NE. Recognition sequence of a restriction enzyme. Nat New Biol 1973, 244(131):7-10. 10.1038/newbio244007a0, 4578426.
25. Geier GE, Modrich P. Recognition sequence of the dam methylase of Escherichia coli K12 and mode of cleavage of Dpn I endonuclease. J Biol Chem 1979, 254(4):1408-1413.
26. Boyer HW, Chow LT, Dugaiczyk A, Hedgpeth J, Goodman HM. DNA substrate site for the EcoRII restriction endonuclease and modification methylase. Nat New Biol 1973, 244(132):40-43. 10.1038/newbio244040a0, 4124385.
27. Kan NC, Lautenberger JA, Edgell MH, Hutchison CA. The nucleotide sequence recognized by the Escherichia coli K12 restriction and modification enzymes. J Mol Biol 1979, 130(2):191-209. 10.1016/0022-2836(79)90426-1, 381674.
28. Kennaway CK, Taylor JE, Song CF, Potrzebowski W, Nicholson W, White JH, Swiderska A, Obarska-Kosinska A, Callow P, Cooper LP, Roberts GA, Artero JB, Bujnicki JM, Trinick J, Kneale GG, Dryden DT. Structure and operation of the DNA-translocating type I DNA restriction enzymes. Genes Dev 2012, 26(1):92-104. 10.1101/gad.179085.111, 3258970, 22215814.
29. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18(5):821-829. 10.1101/gr.074492.107, 2336801, 18349386.
30. Boisvert S, Laviolette F, Corbeil J. Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. J Comput Biol 2010, 17(11):1519-1533. 10.1089/cmb.2009.0238, 3119603, 20958248.
31. Chevreux B, Wetter T, Suhai S. Genome sequence assembly using trace signals and additional sequence information 1999, 45-56. Hannover, Germany: Computer Science and Biology: Proceedings of the German Conference on Bioinformatics.
32. Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol T, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res 2011, 21:2224-2241. 10.1101/gr.126599.111, 3227110, 21926179.
33. Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Giga Sci 2013, In press.
34. Aronesty E. ea-utils Command-line tools for processing biological sequencing data http://code.google.com/p/ea-utils, ea-utils.
35. Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marçais G, Pop M, Yorke JA. GAGE: a critical evaluation of genome assemblies and assembly algorithms. Genome Res 2012, 22(3):557-567. 10.1101/gr.131383.111, 3290791, 22147368.
36. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. Versatile and open software for comparing large genomes. Genome Biol 2004, 5(2):R12. 10.1186/gb-2004-5-2-r12, 395750, 14759262.
37. Phillippy AM, Schatz MC, Pop M. Genome assembly forensics: finding the elusive mis-assembly. Genome Biol 2008, 9(3):R55. 10.1186/gb-2008-9-3-r55, 2397507, 18341692.
38. Narzisi G, Mishra B. Comparing De novo genome assembly: the long and short of it. PLOS One 2011, 6(4):e19175. 10.1371/journal.pone.0019175, 3084767, 21559467.
39. Schadt EE, Banerjee O, Fang G, Feng Z, Wong WH, Zhang X, Kislyuk A, Clark TA, Luong K, Keren-Paz A, Chess A, Kumar V, Chen-Plotkin A, Sondheimer N, Korlach J, Kasarskis A. Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases. Genome Res 2012, 23(1):129-141. 3530673, 23093720.
40. Clark TA, Lu X, Luong K, Dai Q, Boitano M, Turner SW, He C, Korlach J. Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via Tet1 oxidation. BMC Biol 2013, 11:4. 10.1186/1741-7007-11-4, 3598637, 23339471.
41. Wion D, Casadesus J. N6-methyl-adenine: an epigenetic signal for DNA-protein interactions. Nat Rev Microbiol 2006, 4(3):183-192. 10.1038/nrmicro1350, 2755769, 16489347.
42. Nagarajan N, Pop M. Sequence assembly demystified. Nat Rev 2013, 14:157-167.
43. Ribeiro FJ, Przybylski D, Yin S, Sharpe T, Gnerre S, Abouelleil A, Berlin AM, Montmayeur A, Shea TP, Walker BJ, Young SK, Russ C, Nusbaum C, MacCallum I, Jaffe DB. Finished bacterial genomes from shotgun sequence data. Genome Res 2012, 22(11):2270-2277. 10.1101/gr.141515.112, 3483556, 22829535.
44. Kahramanoglou C, Prieto AI, Khedkar S, Haase B, Gupta A, Benes V, Fraser GM, Luscombe NM, Seshasayee A. Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription. Nat Commun 2012, 3:886.
45. Illumina, Inc CASAVA http://support.illumina.com/sequencing/sequencing_software/casava.ilmn, Illumina, Inc.
46. Aronesty E. Comparison of sequencing utility programs. Open Bioinform J 2013, 7:1-8.
47. Chaisson MJ, Tesler G. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): theory and application. BMC Bioinforma 2012, 13:238.
48. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. Circos: an information aesthetic for comparative genomics. Genome Res 2009, 19:1639-1645. 10.1101/gr.092759.109, 2752132, 19541911.