Artifactual pyrosequencing reads in multiple-displacement-amplified sediment metagenomes fromthe Red Sea

PeerJ

Volumn 2013, Issue 1, 2013, Pages

  Wang, Yong ^a   Lee, On On ^a   Yang, Jiang Ke ^a   Li, Tie Gang ^b   Qian, Pei Yuan ^a  

^a HONG KONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Hong Kong)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

Author keywords

Artifactual 454 reads; Gene fragments; MDA; Metagenome

Indexed keywords

ARTICLE; BURKHOLDERIA AMBIFARIA; CONTROLLED STUDY; CUPRIAVIDUS NECATOR; DNA EXTRACTION; GENE STRUCTURE; GENE TRANSLOCATION; METAGENOME; METHYLOBACTERIUM; MOLECULAR BIOLOGY; MULTIPLE DISPLACEMENT AMPLIFICATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PYROSEQUENCING; SEA; SEDIMENT;

EID: 84877144354     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.69     Document Type: Article

References (25)

1. Biddle JF, Fitz-Gibbon S, Schuster SC, Brenchley JE, House CH. 2008. Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. Proceedings of the National Academy of Sciences of the United States of America 105:10583-10588.
2. Biddle JF,White JR, Teske AP, House CH. 2011. Metagenomics of the subsurface Brazos-Trinity Basin (IODP site 1320): comparison with other sediment and pyrosequenced metagenomes. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 5:1038-1047.
3. Borin S, Crotti E,Mapelli F, Tamagnini I, Corselli C, Daffonchio D. 2008. DNA is preserved and maintains transforming potential after contact with brines of the deep anoxic hypersaline lakes of the Eastern Mediterranean Sea. Saline Systems 4:10.
4. Dean FB, Hosono S, Fang L,Wu X, Faruqi AF, Bray-Ward P, Sun Z, Zong Q, Du Y, Du J, Driscoll M, Song W, Kingsmore SF, Egholm M, Lasken RS. 2002. Comprehensive human genome amplification using multiple displacement amplification. Proceedings of the National Academy of Sciences of the United States of America 99:5261-5266.
5. Dean FB, Nelson JR, Giesler TL, Lasken RS. 2001. Rapid amplification of plasmid and phage DNA using phi29 DNA polymerase and multiply-primed rolling circle amplification. Genome Research 11:1095-1099.
6. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32:1792-1797.
7. Ferrer M,Werner J, Chernikova TN, Bargiela R, Fernández L, La Cono V,Waldmann J, Teeling H, Golyshina OV, Glöckner FO, Yakimov MM, Golyshin PN, The MSC. 2012. Unveiling microbial life in the new deep-sea hypersaline Lake Thetis. Part II: a metagenomic study. Environmental Microbiology 14:268-281.
8. Gomez-Alvarez V, Teal TK, Schmidt TM. 2009. Systematic artifacts in metagenomes from complex microbial communities. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 3:1314-1317.
9. Huse S, Huber J,Morrison H, Sogin M,Welch D. 2007. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biology 8:R143.
10. Huse SM, Dethlefsen L, Huber JA,Welch DM, Relman DA, Sogin ML. 2008. Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genetics 4:e1000255.
11. Inskeep WP, Rusch DB, Jay ZJ, Herrgard MJ, Kozubal MA, Richardson TH,Macur RE, Hamamura N, Jennings Rd, Fouke BW, Reysenbach A-L, Roberto F, Young M, Schwartz A, Boyd ES, Badger JH,Mathur EJ, Ortmann AC, Bateson M, Geesey G, Frazier M. 2010. Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function. PLoS ONE 5:e9773.
12. Lasken R, Stockwell T. 2007. Mechanism of chimera formation during the Multiple Displacement Amplification reaction. BMC Biotechnology 7:19.
13. Levy-Booth DJ, Campbell RG, Gulden RH, Hart MM, Powell JR, Klironomos JN, Pauls KP, Swanton CJ, Trevors JT, Dunfield KE. 2007. Cycling of extracellular DNA in the soil environment. Soil Biology and Biochemistry 39:2977-2991.
14. Logares R, Haverkamp THA, Kumar S, Lanźen A, Nederbragt AJ, Quince C, Kauserud H. 2012. Environmental microbiology through the lens of high-throughput DNA sequencing: synopsis of current platforms and bioinformatics approaches. Journal of Microbiological Methods 91:106-113.
15. Markham NR, Zuker M. 2008. UNAFold: software for nucleic acid folding and hybridization. Methods in Molecular Biology 453:3-31.
16. Niu B, Fu L, Sun S, Li W. 2010. Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics 11:187.
17. Pan X, Urban AE, Palejev D, Schulz V, Grubert F, Hu Y, Snyder M,Weissman SM. 2008. A procedure for highly specific, sensitive, and unbiased whole-genome amplification. Proceedings of the National Academy of Sciences of the United States of America 105:15499-15504.
18. Pietramellara G, Ascher J, Borgogni F, Ceccherini M, Guerri G, Nannipieri P. 2009. Extracellular DNA in soil and sediment: fate and ecological relevance. Biology and Fertility of Soils 45:219-235.
19. Quail M, Smith M, Coupland P, Otto T, Harris S, Connor T, Bertoni A, Swerdlow H, Gu Y. 2012. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 13:341.
20. Singh AH, Doerks T, Letunic I, Raes J, Bork P. 2009. Discovering functional novelty in metagenomes: examples from light-mediated processes. Journal of Bacteriology 191:32-41.
21. Spits C, Le Caignec C, De Rycke M, Van Haute L, Van SteirteghemA, Liebaers I, Sermon K. 2006. Optimization and evaluation of single-cell whole-genome multiple displacement amplification. Human Mutation 27:496-503.
22. Steinberger RE, Holden PA. 2005. Extracellular DNA in single- and multiple-species unsaturated biofilms. Applied and Environmental Microbiology 71:5404-5410.
23. Swift SA, Bower AS, Schmitt RW. 2012. Vertical, horizontal, and temporal changes in temperature in the Atlantis II and Discovery hot brine pools. Deep Sea Research Part I: Oceanographic Research Papers 64:118-128.
24. Zhang K,Martiny AC, Reppas NB, Barry KW,Malek J, Chisholm SW, Church GM. 2006. Sequencing genomes from single cells by polymerase cloning. Nature Biotechnology 24:680-686.
25. Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research 31:3406-3415.