Towards next-generation biodiversity assessment using DNA metabarcoding

Molecular Ecology

Volumn 21, Issue 8, 2012, Pages 2045-2050

  Taberlet, Pierre ^a   Coissac, Eric ^a   Pompanon, François ^a   Brochmann, Christian ^b   Willerslev, Eske ^c  

^a UNIVERSITÉ JOSEPH FOURIER   (France)

^b UNIVERSITY OF OSLO   (Norway)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

capture probes; DNA based species identification; next generation DNA sequencing

Indexed keywords

ARTICLE; BIODIVERSITY; DNA BARCODING; DNA SEQUENCE; ECOLOGY; ECOSYSTEM; ENVIRONMENTAL MONITORING; METHODOLOGY; SPECIES DIFFERENCE;

BIODIVERSITY; DNA BARCODING, TAXONOMIC; ECOLOGY; ECOSYSTEM; ENVIRONMENTAL MONITORING; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 84859598363     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2012.05470.x     Document Type: Article

References (56)

1. Andersen K, Bird KL, Rasmussen M, et al. (2012) Meta-barcoding of 'dirt' DNA from soil reflects vertebrate biodiversity. Molecular Ecology, 21, 1966-1979.
2. Avila-Arcos MC, Cappellini E, Romero-Navarro JA, et al. (2011) Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA. Scientific Reports, 1, 74. doi:.
3. Bellemain E, Carlsen T, Brochmann C, et al. (2010) ITS as DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiology, 10, 189.
4. Bienert R, de Danieli S, Miquel C, et al. (2012) Tracking earthworm communities from soil DNA. Molecular Ecology, 21, 2017-2030.
5. Binladen J, Gilbert MTP, Bollback JP, et al. (2007) The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS ONE, 2, e197.
6. Boessenkool S, Epp L, Haile J, et al. (2012) Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA. Molecular Ecology, 21, 1806-1815.
7. Bowman CM, (1986) Copy numbers of chloroplast and nuclear genomes are proportional in mature mesophyll cells of Triticum and Aegilops species. Planta, 167, 264-274.
8. Briggs AW, Good JM, Green RE, et al. (2009) Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science, 325, 318-321.
9. Chariton AA, Court LN, Hartley DM, Colloff MJ, Hardy CM, (2010) Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA. Frontiers in Ecology and the Environment, 8, 233-238.
10. Cline J, Braman JC, Hogrefe HH, (1996) PCR fidelity of Pfu DNA polymerase and other thermostable DNA polymerases. Nucleic Acids Research, 24, 3546-3551.
11. Creer S, Fonseca VG, Porazinska DL, et al. (2010) Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promise. Molecular Ecology, 19, 4-20.
12. Cronin MA, Palmisciano DA, Vyse ER, Cameron DG, (1991) Mitochondrial DNA in wildlife forensic science: species identification of tissues. Wildlife Society Bulletin, 19, 94-105.
13. Curran J, Webster JM, (1987) Identification of nematodes using restriction fragment length differences and species-specific DNA probes. Canadian Journal of Plant Pathology-Revue Canadienne de Phytopathologie, 9, 162-166.
14. Epp L, Boessenkool S, Bellemain E, et al. (2012) New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems. Molecular Ecology, 21, 1821-1833.
15. Ficetola GF, Coissac E, Zundel S, et al. (2010) An in silico approach for the evaluation of DNA barcodes. BMC Genomics, 11, 434.
16. Gale KR, Crampton JM, (1987) DNA probes for species identification of mosquitos in the Anopheles gambiae complex. Medical and Veterinary Entomology, 1, 127-136.
17. Gibson WC, Dukes P, Gashumba JK, (1988) Species-specific DNA probes for the identification of African trypanosomes in tsetse flies. Parasitology, 97, 63-73.
18. Glenn TC, (2011) Field guide to next-generation DNA sequencers. Molecular Ecology Resources, 11, 759-769.
19. Haile J, Froese DG, MacPhee RDE, et al. (2009) Ancient DNA reveals late survival of mammoth and horse in interior Alaska. Proceedings of the National Academy of Sciences of the United States of America, 106, 22352-22357.
20. Hajibabaei M, Shokralla S, Zhou X, Singer GAC, Baird DJ, (2011) Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS One, 6, e17497.
21. Hansen AJ, Mitchel DL, Wiuf C, et al. (2006) Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments. Genetics, 173, 1175-1179.
22. Hauge XY, Litt M, (1993) A study of the origin of 'shadow bands' seen when typing dinucleotide repeat polymorphisms by the PCR. Human Molecular Genetics, 2, 411-415.
23. Hebert PDN, Cywinska A, Ball SL, deWaard JR, (2003) Biological identification through DNA barcodes. Proceedings of the Royal Society of London Series B-Biological Sciences, 270, 313-321.
24. Hodges E, Xuan Z, Balija V, et al. (2007) Genome-wide in situ exon capture for selective resequencing. Nature Genetics, 39, 1522-1527.
25. Hodges E, Rooks M, Xuan ZY, et al. (2009) Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing. Nature Protocols, 4, 960-974.
26. Hollingsworth PM, Forrest LL, Spouge JL, et al. (2009) A DNA barcode for land plants. Proceedings of the National Academy of Sciences of the United States of America, 106, 12794-12797.
27. Jørgensen T, Haile J, Möller P, et al. (2012a) A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational. Molecular Ecology, 21, 1989-2003.
28. Jørgensen T, Kjær KH, Haile J, et al. (2012b) Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records and sedimentary ancient DNA Meta-barcoding. Molecular Ecology, 1980-1988.
29. Kocher TD, Thomas WK, Meyer A, et al. (1989) Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proceedings of the National Academy of Sciences of the United States of America, 86, 6196-6200.
30. Litt M, Hauge X, Sharma V, (1993) Shadow bands seen when typing polymorphic dinucleotide repeats: some causes and cures. BioTechniques, 15, 280-284.
31. Moore MJ, Dhingra A, Soltis PS, et al. (2006) Rapid and accurate pyrosequencing of angiosperm plastid genomes. BMC Plant Biology, 6, 17.
32. Mullis KB, Faloona FA, (1987) Specific synthesis of DNA in vitro via a polymerase-catalysed chain reaction. Methods in Enzymology, 155, 335-350.
33. Murray V, Monchawin C, England PR, (1993) The determination of the sequences present in the shadow bands of a dinucleotide repeat PCR. Nucleic Acids Research, 21, 2395-2398.
34. Nock CJ, Waters DLE, Edwards MA, et al. (2011) Chloroplast genome sequences from total DNA for plant identification. Plant Biotechnology Journal, 9, 328-333.
35. Petit RJ, Excoffier L, (2009) Gene flow and species delimitation. Trends in Ecology & Evolution, 24, 386-393.
36. Pompanon F, Deagle BE, Symondson WOC, et al. (2012) Who is eating what: diet assessment using next generation sequencing. Molecular Ecology, 21, 1931-1950.
37. Porazinska DL, Giblin-Davis RM, Esquivel A, et al. (2010) Ecometagenetics confirms high tropical rainforest nematode diversity. Molecular Ecology, 19, 5521-5530.
38. Riaz T, Shehzad W, Viari A, et al. (2011) ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids Research, 39, e145
39. Rieseberg LH, Soltis DE, (1991) Phylogenetic consequences of cytoplasmic gene flow in plants. Evolutionary Trends in Plants, 5, 65-84.
40. Riesenfeld CS, Schloss PD, Handelsman J, (2004) Metagenomics: genomic analysis of microbial communities. Annual Review of Genetics, 38, 525-552.
41. Rubinoff D, Cameron S, Will K, (2006) A genomic perspective on the shortcomings of mitochondrial DNA for "barcoding" identification. Journal of Heredity, 97, 581-594.
42. Saiki RK, Gelfand DH, Stoffel S, et al. (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science, 239, 487-491.
43. 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, 21, 1951-1965.
44. Shendure J, Ji H, (2008) Next-generation DNA sequencing. Nature Biotechnology, 26, 1035-1045.
45. Sønstebø JH, Gielly L, Brysting A, et al. (2010) A minimalist DNA barcoding approach for reconstructing past Arctic vegetation and climate. Molecular Ecology Resources, 10, 1009-1018.
46. Taberlet P, Gielly L, Pautou G, Bouvet J, (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology, 17, 1105-1109.
47. Taberlet P, Coissac E, Pompanon F, et al. (2007) Power and limitations of the chloroplast trnL(UAA) intron for plant DNA barcoding. Nucleic Acids Research, 35, e14.
48. Teletchea F, Bernillon J, Duffraisse M, Laudet V, Hanni C, (2008) Molecular identification of vertebrate species by oligonucleotide microarray in food and forensic samples. Journal of Applied Ecology, 45, 967-975.
49. Timmermans MJTN, Dodsworth S, Culverwell CL, et al. (2010) Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics. Nucleic Acids Research, 38, e197.
50. Tringe SG, von Mering C, Kobayashi A, et al. (2005) Comparative metagenomics of microbial communities. Science, 308, 554-557.
51. 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.
52. Will KW, Mishler BD, Wheeler QD, (2005) The perils of DNA barcoding and the need for integrative taxonomy. Systematic Biology, 54, 844-851.
53. Willerslev E, Hansen AJ, Binladen J, et al. (2003) Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science, 300, 791-795.
54. Willerslev E, Hansen AJ, Poinar HN, (2004) Isolation of nucleic acids and cultures from fossil ice and permafrost. Trends in Ecology & Evolution, 19, 141-147.
55. Willerslev E, Cappellini E, Boomsma W, et al. (2007) Ancient biomolecules from deep ice cores reveal a forested Southern Greenland. Science, 317, 111-114.
56. Yoccoz NG, Bråthen KA, Gielly L, et al. (2012) DNA from soil mirrors plant taxonomic and growth form diversity. Molecular Ecology, 10.1111/j.1365-294X.2012.05545.x.