Selective whole genome amplification for resequencing target microbial species from complex natural samples

Genetics

Volumn 198, Issue 2, 2014, Pages 473-481

  Leichty, Aaron R ^a   Brisson, Dustin ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; BACTERIAL DNA;

ARTICLE; BORRELIA BURGDORFERI; CHIMERA; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; ESCHERICHIA COLI; GENE AMPLIFICATION; GENE DOSAGE; GENE MAPPING; MICROBIAL COMMUNITY; MICROBIAL GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; POINT MUTATION; POPULATION GENETICS; SELECTIVE WHOLE GENOME AMPLIFICATION; TARGET ORGANISM; WOLBACHIA PIPIENTIS; ANIMAL; BACTERIAL GENOME; DNA SEQUENCE; FEMALE; GENE LIBRARY; GENETICS; MICROBIOLOGY; NUCLEIC ACID AMPLIFICATION;

ANIMALS; BORRELIA BURGDORFERI; DNA, BACTERIAL; DROSOPHILA MELANOGASTER; ENVIRONMENTAL MICROBIOLOGY; ESCHERICHIA COLI; FEMALE; GENE LIBRARY; GENOME, BACTERIAL; NUCLEIC ACID AMPLIFICATION TECHNIQUES; SEQUENCE ANALYSIS, DNA;

EID: 84908052364     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.114.165498     Document Type: Article

References (40)

1. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang et al.,1997 Gapped BLAST and PSI-BLAST: a new generation of proteindatabase search programs. Nucleic Acids Res. 25: 3389–3402.
2. Beerli, P., 2004 Effect of unsampled populations on the estimationof population sizes and migration rates between sampledpopulations. Mol. Ecol. 13: 827–836.
3. Blainey, P. C., 2013 The future is now: single-cell genomics ofbacteria and archaea. FEMS Microbiol. Rev. 37: 407–427.
4. Castro-Nallar, E., M. Perez-Losada, G. F. Burton, and K. A. Crandall, 2012 The evolution of HIV: inferences using phylogenetics.Mol. Phylogenet. Evol. 62: 777–792.
5. Dean, F. B., J. R. Nelson, T. L. Giesler, and R. S. Lasken, 2001 Rapidamplification of plasmid and phage DNA using Phi 29 DNA polymeraseand multiply-primed rolling circle amplification. GenomeRes. 11: 1095–1099.
6. Dean, F. B., S. Hosono, L. Fang, X. Wu, A. F. Faruqi et al., 2002 Comprehensivehuman genome amplification using multiple displacementamplification. Proc. Natl. Acad. Sci. USA 99: 5261–5266.
7. Deng, X., H. Liu, Y. Shao, S. Rayner, and R. Yang, 2008 Theepidemic origin and molecular properties of B9: a founder strainof the HIV-1 transmission in Asia. AIDS 22: 1851–1858.
8. Ellegaard, K. M., L. Klasson, K. Naslund, K. Bourtzis, andS. G. Andersson, 2013 Comparative genomics of Wolbachiaand the bacterial species concept. PLoS Genet. 9:e1003381.
9. Fraser, C. M., S. Casjens, W. M. Huang, G. G. Sutton, R. A. Claytonet al., 1997 Genomic sequence of a Lyme disease spirochaete,Borrelia burgdorferi. Nature 390: 580–586.
10. Fuller, C. W., L. R. Middendorf, S. A. Benner, G. M. Church, T. Harris et al., 2009 The challenges of sequencing by synthesis. Nat. Biotechnol. 27: 1013–1023.
11. Gorski, L., 2012 Selective enrichment media bias the types ofSalmonella enterica strains isolated from mixed strain culturesand complex enrichment broths. PLoS ONE 7: e34722.
12. Grenfell, B. T., O. G. Pybus, J. R. Gog, J. L. Wood, J. M. Daly et al., 2004 Unifying the epidemiological and evolutionary dynamicsof pathogens. Science 303: 327–332.
13. Hofinger, B. J., J. R. Russell, C. G. Bass, T. Baldwin, M. dos Reis et al., 2011 An exceptionally high nucleotide and haplotype diversityand a signature of positive selection for the eIF4E resistance genein barley are revealed by allele mining and phylogenetic analysesof natural populations. Mol. Ecol. 20: 3653–3668.
14. Holmes, E. C., and B. T. Grenfell, 2009 Discovering the phylodynamicsof RNA viruses. PLOS Comput. Biol. 5: e1000505.
15. Hume, J. C., E. J. Lyons, and K. P. Day, 2003 Human migration,mosquitoes and the evolution of Plasmodium falciparum. TrendsParasitol. 19: 144–149.
16. Humphrey, P. T., D. A. Caporale, and D. Brisson, 2010 Uncoordinatedphylogeography of Borrelia burgdorferi and its tick vector, Ixodesscapularis. Evolution 64: 2653–2663.
17. Lam, H. Y., M. J. Clark, R. Chen, R. Chen, G. Natsoulis et al., 2012 Performance comparsion of whole-genome sequencingplatforms. Nat. Biotechnol. 30: 78–82.
18. Langmead, B., and S. L. Salzberg, 2012 Fast gapped-read alignmentwith Bowtie 2. Nat. Methods 9: 357–359.
19. Lasken, R. S., and T. B. Stockwell, 2007 Mechanism of chimeraformation during the Multiple Displacement Amplification reaction. BMC Biotechnol. 7: 19.
20. Li, H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., 2009 The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078–2079.
21. Mardis, E. R., 2008 Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet. 9: 387–402.
22. Marygold, S. J., P. C. Leyland, R. L. Seal, J. L. Goodman, J. Thurmondet al., 2013 FlyBase: improvements to the bibliography. NucleicAcids Res. 41: D751–D757.
23. McLean, J. S., M. J. Lombardo, M. G. Ziegler, M. Novotny, J. Yee-Greenbaum et al., 2013 Genome of the pathogen Porphyromonasgingivalis recovered from a biofilm in a hospital sink using a highthroughputsingle-cell genomics platform. Genome Res. 23: 867–877.
24. Pinard, R., A. de Winter, G. J. Sarkis, M. B. Gerstein, K. R. Tartaroet al., 2006 Assessment of whole genome amplification-inducedbias through high-throughput, massively parallel whole genomesequencing. BMC Genomics 7: 216.
25. Quail, M. A., M. Smith, P. Coupland, T. D. Otto, S. R. Harris et al., 2012 A tale of three next generation sequencing platforms:comparison of Ion Torrent, Pacific Biosciences and IlluminaMiSeq sequencers. BMC Genomics 13: 341.
26. Quinlan, A. R., and I. M. Hall, 2010 BEDTools: a flexible suite ofutilities for comparing genomic features. Bioinformatics 26:841–842.
27. R Development Core Team, 2012 R: A Language and Environmentfor Statistical Computing, R Foundation for Statistical Computing,Vienna.
28. Richardson, M. F., L. A. Weinert, J. J. Welch, R. S. Linheiro, M. M. Magwire et al., 2012 Population genomics of the Wolbachiaendosymbiont in Drosophila melanogaster. PLoS Genet. 8: e1003129.
29. Ritz, C., and A. Spiess, 2008 qpcR: an R package for sigmoidalmodel selection in quantitative real-time polymerase chain reactionanalysis. Bioinformatics 24: 1549–1551.
30. Roberts, R. J., T. Vincze, J. Posfai, and D. Macelis, 2010 REBASE—a database for DNA restriction and modification: enzymes,genes and genomes. Nucleic Acids Res. 38: D234–D236.
31. Rodrigue, S., R. R. Malmstrom, A. M. Berlin, B. W. Birren, M. R. Henn et al., 2009 Whole genome amplification and de novoassembly of single bacterial cells. PLoS ONE 4: e6864.
32. Rosenberg, N. A., and M. Nordborg, 2002 Genealogical trees, coalescenttheory and the analysis of genetic polymorphisms. Nat.Rev. Genet. 3: 380–390.
33. Ross, M. G., C. Russ, M. Costello, A. Hollinger, N. J. Lennon et al., 2013 Characterizing and measuring bias in sequence data.Genome Biol. 14: R51.
34. Schmieder, R., and R. Edwards, 2011 Quality control and preprocessingof metagenomic datasets. Bioinformatics 27: 863–864.
35. Simmons, S., G. Dibartolo, V. Denef, D. Goltsman, M. Thelenet al., 2008 Population genomic analysis of strain variationin Leptospirillum group II bacteria involved in acid mine drainageformation. PLoS Biol. 6: e177.
36. Snyder, J. C., J. Spuhler, B. Wiedenheft, F. F. Roberto, T. Douglaset al., 2004 Effects of culturing on the population structure ofa hyperthermophilic virus. Microb. Ecol. 48: 561–566.
37. Sun, L. V., J. M. Foster, G. Tzertzinis, M. Ono, C. Bandi et al., 2001 Determination of Wolbachia genome size by pulsed-fieldgel electrophoresis. J. Bacteriol. 183: 2219–2225.
38. Wakeley, J., 2004 Recent trends in population genetics: Moredata! More math! Simple models? J. Hered. 95: 397–405.
39. Wilson, D. J., 2012 Insights from genomics into bacterial pathogenpopulations. PLoS Pathog. 8: e1002874.
40. Wu, M., L. V. Sun, J. Vamathevan, M. Riegler, R. Deboy et al., 2004 Phylogenomics of the reproductive parasite Wolbachiapipientis wMel: a streamlined genome overrun by mobile geneticelements. PLoS Biol. 2: E69.