Indexed PCR primers induce template- Specific bias in Large-Scale DNA sequencing studies

PLoS ONE

Volumn 11, Issue 3, 2016, Pages

  O'donnell, James L ^a   Kelly, Ryan P ^a   Lowell, Natalie C ^a   Port, Jesse A ^b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA EXTRACTION; DNA SEQUENCE; GENE AMPLIFICATION; POLYMERASE CHAIN REACTION; GENETICS; HIGH THROUGHPUT SEQUENCING; PROCEDURES; SPECIES DIFFERENCE;

PRIMER DNA;

DNA PRIMERS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 84961182629     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0148698     Document Type: Article

References (38)

1. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, et al. Environmental Genome Shotgun Sequencing of the Sargasso Sea. Science. 2004; 304(5667):66-74. doi: 10.1126/science. 1093857 PMID: 15001713.
2. Iverson V, Morris RM, Frazar CD, Berthiaume CT, Morales RL, Armbrust EV. Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota. Science. 2012; 335 (6068):587-590. doi: 10.1126/science.1212665 PMID: 22301318.
3. Taylor DL, Booth MG, McFarland JW, Herriott IC, Lennon NJ, Nusbaum C, et al. Increasing ecological inference from high throughput sequencing of fungi in the environment through a tagging approach. Molecular Ecology Resources. 2008; 8(4):742-752. doi: 10.1111/j.1755-0998.2008.02094.x PMID: 21585882.
4. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, et al. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proceedings of the National Academy of Sciences of the United States of America. 2006; 103(32):12115-20. doi: 10.1073/pnas.0605127103 PMID: 16880384.
5. Lozupone CA, Knight R. Global patterns in bacterial diversity. Proceedings of the National Academy of Sciences. 2007; 104(27):11436-11440. doi: 10.1073/pnas.0611525104.
6. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, et al. Ultra-high-Throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012; 6(8):1621- 1624. doi: 10.1038/ismej.2012.8 PMID: 22402401.
7. Gibson J, Shokralla S, Porter TM, King I, van Konynenburg S, Janzen DH, et al. Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics. Proceedings of the National Academy of Sciences of the United States of America. 2014; 111 (22):8007-12. doi: 10.1073/pnas.1406468111 PMID: 24808136.
8. Leray M, Yang JY, Meyer CP, Mills SC, Agudelo N, Ranwez V, et al. A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: Application for characterizing coral reef fish gut contents. Frontiers in zoology. 2013; 10(1):34. doi: 10.1186/1742- 9994-10-34 PMID: 23767809.
9. Leray M, Knowlton N. DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity. Proceedings of the National Academy of Sciences. 2015; 112(7):20142-4997. doi: 10.1073/pnas.1424997112.
10. Taberlet P, Coissac E, Pompanon F, Brochmann C, Willerslev E. Towards next-generation biodiversity assessment using DNA metabarcoding. Molecular Ecology. 2012; 21(8):2045-2050. doi: 10.1111/j. 1365-294X.2012.05470.x PMID: 22486824.
11. Valentini A, Taberlet P, Miaud C, Civade R, Herder J, Thomsen PF, et al. Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology. 2015; p. n/a-n/a.
12. Son MS, Taylor RK. Preparing DNA Libraries for Multiplexed Paired-End Deep Sequencing for Illumina GA Sequencers. In: Current Protocols in Microbiology. John Wiley & Sons, Inc.; 2011.
13. Binladen J, Gilbert MTP, Bollback JP, Panitz F, Bendixen C, Nielsen R, et al. The Use of Coded PCR Primers Enables High-Throughput Sequencing of Multiple Homolog Amplification Products by 454 Parallel Sequencing. PLoS ONE. 2007; 2(2):e197. doi: 10.1371/journal.pone.0000197 PMID: 17299583.
14. Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nature methods. 2008; 5(3):235-237. doi: 10.1038/nmeth.1184 PMID: 18264105.
15. Hoffmann C, Minkah N, Leipzig J, Wang G, Arens MQ, Tebas P, et al. DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations. Nucleic Acids Research. 2007; 35(13). doi: 10. 1093/nar/gkm435.
16. Wu JH, Hong PY, Liu WT. Quantitative effects of position and type of single mismatch on single base primer extension. Journal of Microbiological Methods. 2009; 77(3):267-275. doi: 10.1016/j.mimet. 2009.03.001 PMID: 19285527.
17. Suzuki MT, Giovannoni SJ. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Applied and Environmental Microbiology. 1996; 62(2):625-630. PMID: 8593063.
18. Polz MF, Cavanaugh CM. Bias in Template-To-Product Ratios in Multitemplate PCR. Applied and Environmental Microbiology. 1998; 64(10):3724-3730. PMID: 9758791.
19. Wintzingerode FV, Göbel UB, Stackebrandt E. Determination of microbial diversity in environmental samples: Pitfalls of PCR-based rRNA analysis. FEMS Microbiology Reviews. 1997; 21(3):213-229. doi: 10.1111/j.1574-6976.1997.tb00351.x.
20. Sipos R, Székely AJ, Palatinszky M, Révész S, Márialigeti K, Nikolausz M. Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-Targetting bacterial community analysis. FEMS Microbiology Ecology. 2007; 60(2):341-350. doi: 10.1111/j.1574-6941.2007.00283.x PMID: 17343679.
21. Piñol J, Mir G, Gomez-Polo P, Agustí N. Universal and blocking primer mismatches limit the use of high-Throughput DNA sequencing for the quantitative metabarcoding of arthropods. Molecular ecology resources. 2014;.
22. Pinto AJ, Raskin L. PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS ONE. 2012; 7(8). doi: 10.1371/journal.pone.0043093.
23. Berry D, Mahfoudh KB, Wagner M, Loy A. Barcoded primers used in multiplex amplicon pyrosequencing bias amplification. Applied and Environmental Microbiology. 2011; 77(21):7846-7849. doi: 10. 1128/AEM.05220-11 PMID: 21890669.
24. Renshaw MA, Olds BP, Jerde CL, Mcveigh MM, Lodge DM. The room temperature preservation of filtered environmental DNA samples and assimilation into a phenol-chloroform-isoamyl alcohol DNA extraction. Molecular Ecology Resources. 2014;. doi: 10.1111/1755-0998.12281 PMID: 24834966.
25. Riaz T, Shehzad W, Viari A, Pompanon F, Taberlet P, Coissac E. ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids Research. 2011; 39(21):e145- e147. doi: 10.1093/nar/gkr732 PMID: 21930509.
26. Coissac E. OligoTag: A Program for Designing Sets of Tags for Next-Generation Sequencing of Multiplexed Samples. In: Pompanon F, Bonin A, editors. Data Production and Analysis in Population Genomics SE-2. vol. 888 of Methods in Molecular Biology. Humana Press; 2012. p. 13-31. doi: 10.1007/978-1-61779-870-2-2.
27. De Barba M, Miquel C, Boyer F, Mercier C, Rioux D, Coissac E, et al. DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: Application to omnivorous diet. Molecular Ecology Resources. 2014; 14(2):306-323. doi: 10.1111/1755-0998.12188 PMID: 24128180.
28. Schnell IB, Bohmann K, Gilbert MTP. Tag jumps illuminated-reducing sequence-To-sample misidentifications in metabarcoding studies. Molecular Ecology Resources. 2015; p. n/a-n/a.
29. Zhang J, Kobert K, Flouri T, Stamatakis A. PEAR: A fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics. 2014; 30(5):614-620. doi: 10.1093/bioinformatics/btt593 PMID: 24142950.
30. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010; 26 (19):2460-2461. doi: 10.1093/bioinformatics/btq461 PMID: 20709691.
31. Martin M. Cutadapt removes adapter sequences from high-Throughput sequencing reads. EMBnet journal. 2011; 17(1):10.
32. R Core Team. R: A Language and Environment for Statistical Computing; 2014. Available from: http://www.r-project.org/.
33. Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O'Hara RB, et al. vegan: Community Ecology Package; 2015. Available from: http://cran.r-project.org/package=vegan.
34. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: Architecture and applications. BMC bioinformatics. 2009; 10:421. doi: 10.1186/1471-2105-10-421 PMID: 20003500.
35. Shelton AO, O'Donnell JL, Samhouri JF, Lowell NC, Williams GD, Kelly RP. A framework for inferring biological communities from environmental DNA. Ecological Applications;.
36. Lahoz-Monfort JJ, Guillera-Arroita G, Tingley R. Statistical approaches to account for false positive errors in environmental DNA samples. Molecular Ecology Resources. 2015; p. n/a-n/a. doi: 10.1111/1755-0998.12486.
37. Bellemain E, Carlsen T, Brochmann C, Coissac E, Taberlet P, Kauserud H. ITS as an environmental DNA barcode for fungi: An in silico approach reveals potential PCR biases. BMC microbiology. 2010; 10:189. doi: 10.1186/1471-2180-10-189 PMID: 20618939.
38. Ficetola GF, Pansu J, Bonin A, Coissac E, Giguet-Covex C, De Barba M, et al. Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data. Molecular Ecology Resources. 2014; p. n/a-n/a.