Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods

Molecular Ecology Resources

Volumn 15, Issue 4, 2015, Pages 819-830

  Piñol, Josep ^a,b   Mir, G ^c,d   Gomez Polo, P ^e   Agusti N ^e  

^a UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^b CREAF   (Spain)

^c CSIC   (Spain)

^d PETER MACCALLUM CANCER CENTRE   (Australia)

^e IRTA   (Spain)

Author keywords

Annealing temperature; Insects; Ion Torrent; PCR bias; PCR cycles

Indexed keywords

ARTHROPODA; HEXAPODA;

PRIMER DNA;

ANIMAL; ARTHROPOD; BASE MISPAIRING; CLASSIFICATION; DIAGNOSTIC ERROR; DNA BARCODING; DNA SEQUENCE; GENETICS; HIGH THROUGHPUT SEQUENCING; MOLECULAR GENETICS; POLYMERASE CHAIN REACTION; PROCEDURES;

ANIMALS; ARTHROPODS; BASE PAIR MISMATCH; DIAGNOSTIC ERRORS; DNA BARCODING, TAXONOMIC; DNA PRIMERS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

EID: 84931956994     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12355     Document Type: Article

References (47)

1. Amend AS, Seifert KA, Bruns TD (2010) Quantifying microbial communities with 454 pyrosequencing: does read abundance count? Molecular Ecology, 19, 5555-5565.
2. Bohmann K, Monadjem A, Noer CL et al. (2011) Molecular dietary analysis of two African free-tailed bats (Molossidae) using high throughput sequencing. PLoS ONE, 6, e21441.
3. Brown DS, Jarman SN, Symondson WOC (2012) Pyrosequencing of prey DNA in reptile faeces: analysis of earthworm consumption by slow worms. Molecular Ecology Resources, 12, 259-266.
4. Carew ME, Pettigrove VJ, Metzeling L, Hoffmann AA (2013) Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species. Frontiers in Zoology, 10, 45.
5. Clarke LJ, Soubrier J, Weyrich LS, Cooper A (2014) Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias. Molecular Ecology Resources, 14, 1160-1170.
6. De Barba M, Miquel C, Boyer C et al. (2014) DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet. Molecular Ecology Resources, 14, 306-323.
7. Deagle BE, Kirkwood R, Jarman SN (2009) Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces. Molecular Ecology, 18, 2022-2038.
8. Deagle BE, Chiaradia A, McInnes J, Jarman SN (2010) Pyrosequencing faecal DNA to determine diet of little penguins: is what goes in what comes out? Conservation Genetics, 11, 2039-2048.
9. Deagle BE, Thomas AC, Shaffer AK, Trites AW, Jarman SN (2013) Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count? Molecular Ecology Resources, 13, 620-633.
10. Egge E, Bittner L, Andersen T, Audic S, de Vargas C, Edvardsen B (2013) 454 pyrosequencing to describe microbial eukaryotic community composition, diversity and relative abundance: a test for marine haptophytes. PLoS ONE, 8, e74371.
11. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology, 3, 294-299.
12. Forney LJ, Zhou X, Brown CJ (2004) Molecular microbial ecology: land of the one-eyed king. Current Opinion in Microbiology, 7, 210-220.
13. Fouts DE, Szpakowski S, Purushe J et al. (2012) Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen. PLoS ONE, 7, e48289.
14. Gregory TR (2014). Animal Genome Size Database. http://www.genomesize.com.
15. Hiiesalu I, Pik MO, Metsis M et al. (2012) Plant species richness belowground: higher richness and new patterns revealed by next-generation sequencing. Molecular Ecology, 21, 2004-2016.
16. Huson DH, Mitra S, Ruscheweyh HJ, Weber N, Schuster SC (2011) Integrative analysis of environmental sequences using MEGAN 4. Genome Research, 21, 1552-1560.
17. Kelly RP, Port JA, Yamahara KM, Crowder LB (2014) Using environmental DNA to census marine fishes in a large mesocosm. PLoS ONE, 9, e86175.
18. Kowalczyk R, Taberlet P, Coissac E et al. (2011) Influence of management practices on large herbivore diet-Case of European bison in Białowiez˙a Primeval Forest (Poland). Forest Ecology and Management, 261, 821-828.
19. Kwok S, Kellogg DE, McKinney N et al. (1990) Effects of primer-template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies. Nucleic Acids Research, 18, 999-1005.
20. Leray M, Yang JY, Meyer CP et al. (2013) 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, 10, 34.
21. McPherson M, Moller S (2006) PCR, 2nd edn. Taylor & Francis, London.
22. Meusnier I, Singer GAC, Landry JF, Hickey DA, Hebert PDN, Hajibabaei M (2008) A universal mini-barcode for biodiversity analysis. BMC Genomics, 9, 214.
23. Piñol J, San Andrés V, Clare EL, Mir G, Symondson WOC (2014) A pragmatic approach to the analysis of diets of generalist predators: the use of next generation sequencing with no blocking probes. Molecular Ecology Resources, 14, 18-26.
24. Pinto AJ, Raskin L (2012) PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS ONE, 7, e43093.
25. Pochon X, Bott NJ, Smith KF, Wood SA (2013) Evaluating detection limits of next-generation sequencing for the surveillance and monitoring of international marine pests. PLoS ONE, 8, e73935.
26. Polz MF, Cavanaugh CM (1998) Bias in template-to-product ratios in multitemplate PCR. Applied and Environmental Microbiology, 64, 3724-3730.
27. Porazinska DL, Giblin-Davis RM, Faller L et al. (2009) Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity. Molecular Ecology Resources, 9, 1439-1450.
28. Porazinska DL, Sung W, Giblin-Davis RM, Thomas WK (2010) Reproducibility of read numbers in high-throughput sequencing analysis of nematode community composition and structure. Molecular Ecology Resources, 10, 666-676.
29. Quail MA, Smith M, Coupland P et al. (2012) A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics, 13, 341.
30. R Core Team (2012). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org/.
31. Raye G, Miquel M, Coissac E, Redjadj C, Loison A, Taberlet P (2011) New insights on diet variability revealed by DNA barcoding and high-throughput pyrosequencing: chamois diet in autumn as a case study. Ecological Research, 26, 265-276.
32. Schmieder R, Edwards R (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics, 27, 863-864.
33. Schmieder R, Lim YW, Rohwer F, Edwards R (2011) TagCleaner: identification and removal of tag sequences from genomic and metagenomic datasets. BMC Bioinformatics, 11, 341.
34. Shehzad W, Riaz T, Nawaz MA et al. (2012) Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan. Molecular Ecology, 8, 1951-1965.
35. Sipos R, Székely AJ, Palatinszky M, Révész S, Márialigeti K, Nikolausz M (2007) Effect of primer mismatch, annealing temperature and PCR cycle number on16S rRNA gene-targeting bacterial community analysis. FEMS Microbiology Ecology, 60, 341-350.
36. Sogin ML, Morrison HG, Huber JA et al. (2006) Microbial diversity in the deep sea and the underexplored 'rare biosphere'. PNAS, 103, 12115-12120.
37. Soininen EM, Valentini A, Coissac E et al. (2009) Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures. Frontiers in Zoology, 6, 16.
38. Steele RE, Pires JC (2011) Biodiversity assessment: state-of-the-art techniques in phylogenomics and species identification. American Journal of Botany, 98, 415-425.
39. Taberlet P, Coissac E, Pompanon F, Brochmann C, Willerslev E (2012) Towards next-generation biodiversity assessment using DNA metabarcoding. Molecular Ecology, 21, 2045-2050.
40. Valentini A, Miquel C, Nawaz MA et al. (2009) New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach. Molecular Ecology Resources, 9, 51-60.
41. Vestheim H, Jarman SN (2008) Blocking primers to enhance PCR amplification of rare sequences in mixed samples - a case study on prey DNA in Antarctic krill stomachs. Frontiers in Zoology, 5, 12.
42. Wintzingerode FV, Göbel UV, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiology Reviews, 21, 213-229.
43. Xu L, Ravnskov S, Larsen J, Nilsson RH, Nicolaisen M (2012) Soil fungal community structure along a soil health gradient in pea fields examined using deep amplicon sequencing. Soil Biology and Biochemistry, 46, 26e32.
44. Yu DW, Ji Y, Emerson BC et al. (2012) Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods in Ecology and Evolution, 3, 613-623.
45. Zeale MRK, Butlin RK, Barker GLA, Lees DC, Jones G (2011) Taxon-specific PCR for DNA barcoding arthropod prey in bat faeces. Molecular Ecology Resources, 11, 236-244.
46. Zhang Z, Schwartz S, Wagner L, Miller W (2000) A greedy algorithm for aligning DNA sequences. Journal of Computational Biology, 7, 203-214.
47. Zhou X, Li Y, Liu S et al. (2013) Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification. GigaScience, 2, 4.