Conservation of gene cassettes among diverse viruses of the human gut

PLoS ONE

Volumn 7, Issue 8, 2012, Pages

  Minot, Samuel ^a   Wu, Gary D ^a   Lewis, James D ^a   Bushman, Frederic D ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; CONTIG; NUCLEOTIDE; VIRUS DNA; VIRUS PROTEIN;

ACCESS TO INFORMATION; ARTICLE; BACTERIOPHAGE; COMPUTER PROGRAM; DNA SEQUENCE; GENE CASSETTE; GENE ORDER; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC CONSERVATION; INTERNET; INTESTINE FLORA; METAGENOMICS; OPEN READING FRAME; PROTEIN DATABASE; PROTEIN MOTIF; VIRUS GENE;

BACTERIOPHAGES; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; CONTIG MAPPING; GENOME, VIRAL; HUMANS; INTESTINES; METAGENOME; OPEN READING FRAMES; VIRAL PROTEINS;

EID: 84865013146     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0042342     Document Type: Article

References (49)

1. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65.
2. Reyes A, Haynes M, Hanson N, Angly FE, Heath AC, et al. (2010) Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466: 334-338.
3. Minot S, Sinha R, Chen J, Li H, Keilbaugh SA, et al. (2011) The human gut virome: Inter-individual variation and dynamic response to diet. Genome Res 21: 1616-1625.
4. Kingsford C, Schatz MC, Pop M, (2010) Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics 11: 21.
5. Charuvaka A, Rangwala H, (2011) Evaluation of short read metagenomic assembly. BMC Genomics 12 Suppl 2: S8.
6. Luo C, Tsementzi D, Kyrpides NC, Konstantinidis KT (2011) Individual genome assembly from complex community short-read metagenomic datasets. ISME J.
7. Pignatelli M, Moya A, (2011) Evaluating the fidelity of de novo short read metagenomic assembly using simulated data. PLoS One 6: e19984.
8. Rohwer F, (2003) Global phage diversity. Cell 113: 141.
9. Breitbart M, Haynes M, Kelley S, Angly F, Edwards RA, et al. (2008) Viral diversity and dynamics in an infant gut. Res Microbiol 159: 367-373.
10. Breitbart M, Hewson I, Felts B, Mahaffy JM, Nulton J, et al. (2003) Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol 185: 6220-6223.
11. Minot S, Grunberg S, Wu GD, Lewis JD, Bushman FD (2012) Hypervariable loci in the human gut virome. Proc Natl Acad Sci U S A.
12. Petrov VM, Ratnayaka S, Nolan JM, Miller ES, Karam JD, (2010) Genomes of the T4-related bacteriophages as windows on microbial genome evolution. Virol J 7: 292.
13. Rohwer F, Edwards R, (2002) The Phage Proteomic Tree: a genome-based taxonomy for phage. J Bacteriol 184: 4529-4535.
14. Arslan D, Legendre M, Seltzer V, Abergel C, Claverie JM, (2011) Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae. Proc Natl Acad Sci U S A 108: 17486-17491.
15. Rodriguez-Valera F, Martin-Cuadrado AB, Rodriguez-Brito B, Pasic L, Thingstad TF, et al. (2009) Explaining microbial population genomics through phage predation. Nat Rev Microbiol 7: 828-836.
16. Hoffmann KH, Rodriguez-Brito B, Breitbart M, Bangor D, Angly F, et al. (2007) Power law rank-abundance models for marine phage communities. FEMS Microbiol Lett 273: 224-228.
17. Lima-Mendez G, Toussaint A, Leplae R, (2011) A modular view of the bacteriophage genomic space: identification of host and lifestyle marker modules. Res Microbiol 162: 737-746.
18. Lucchini S, Desiere F, Brussow H, (1999) Comparative genomics of Streptococcus thermophilus phage species supports a modular evolution theory. J Virol 73: 8647-8656.
19. Botstein D, (1980) A theory of modular evolution for bacteriophages. Ann N Y Acad Sci 354: 484-490.
20. Sanger F, Coulson AR, Friedmann T, Air GM, Barrell BG, et al. (1978) The nucleotide sequence of bacteriophage phiX174. J Mol Biol 125: 225-246.
21. Rao VB, Black LW (2005) DNA packaging in bacteriophage T4. In: Catalano C, editor. Viral Genome Packaging Machines. Georgetown, TX: Landes Bioscience. 40-58.
22. Miller JR, Koren S, Sutton G, (2010) Assembly algorithms for next-generation sequencing data. Genomics 95: 315-327.
23. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, et al. (2009) ABySS: a parallel assembler for short read sequence data. Genome Res 19: 1117-1123.
24. Zerbino DR, Birney E, (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829.
25. Li R, Zhu H, Ruan J, Qian W, Fang X, et al. (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20: 265-272.
26. Zhang W, Chen J, Yang Y, Tang Y, Shang J, et al. (2011) A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies. PLoS One 6: e17915.
27. Lin Y, Li J, Shen H, Zhang L, Papasian CJ, et al. (2011) Comparative studies of de novo assembly tools for next-generation sequencing technologies. Bioinformatics 27: 2031-2037.
28. Pevzner PA, Tang H, Waterman MS, (2001) An Eulerian path approach to DNA fragment assembly. Proc Natl Acad Sci U S A 98: 9748-9753.
29. Peng Y, Leung HC, Yiu SM, Chin FY, (2011) Meta-IDBA: a de Novo assembler for metagenomic data. Bioinformatics 27: i94-101.
30. Peng Y, Leung HC, Yiu SM, Chin FY, (2010) IDBA- A Practical Iterative de Bruijn Graph De Novo Assembler. Research in Computational Molecular Biology 6044: 426-440.
31. Ng TF, Willner DL, Lim YW, Schmieder R, Chau B, et al. (2011) Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes. PLoS One 6: e20579.
32. Willner D, Furlan M, Schmieder R, Grasis JA, Pride DT, et al. (2011) Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity. Proc Natl Acad Sci U S A 108 Suppl 1: 4547-4553.
33. Botstein D, Herskowitz I, (1974) Properties of hybrids between Salmonella phage P22 and coliphage lambda. Nature 251: 584-589.
34. Hendrix RW, Roberts JW, Stahl FW, Weisberg RA (1983) Lambda II. Cold Spring Harbor: Cold Spring Harbor Laboratory.
35. Hershey AD (1971) The Bacteriophage Lambda. Cold Spring Harbor Laboratory, New York: Cold Spring Harbor Press.
36. Wilgus GS, Mural RJ, Friedman DI, Fiandt M, Szybalski W, (1973) Lambda imm lambda-434: a phage with a hybrid immunity region. Virology 56: 46-53.
37. Leiman PG, Shneider MM, (2012) Contractile tail machines of bacteriophages. Adv Exp Med Biol 726: 93-114.
38. Shah SA, Garrett RA, (2011) CRISPR/Cas and Cmr modules, mobility and evolution of adaptive immune systems. Res Microbiol 162: 27-38.
39. Sauer RT, Yocum RR, Doolittle RF, Lewis M, Pabo CO, (1982) Homology among DNA-binding proteins suggests use of a conserved super-secondary structure. Nature 298: 447-451.
40. Ohlendorf DH, Anderson WF, Lewis M, Pabo CO, Matthews BW, (1983) Comparison of the structures of cro and lambda repressor proteins from bacteriophage lambda. J Mol Biol 169: 757-769.
41. Ptashne M (1986) A Genetic Switch. Cambridge, Massachusetts: Cell and Blackwell Scientific Press.
42. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
43. Thurber RV, Haynes M, Breitbart M, Wegley L, Rohwer F, (2009) Laboratory procedures to generate viral metagenomes. Nat Protoc 4: 470-483.
44. Pruitt K, Brown G, Tatusova T, Maglott D (2011) The Reference Sequence (RefSeq) Database. In: McEntyre J, Ostell J, editors. The NCBI Handbook. Bethesda, MD: National Center for Biotechnology Information.
45. Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, et al. (2011) CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 39: D225-229.
46. Delcher AL, Bratke KA, Powers EC, Salzberg SL, (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673-679.
47. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, et al. (2009) BLAST+: architecture and applications. BMC Bioinformatics 10: 421.
48. Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T, (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27: 431-432.
49. Edgar RC, (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.