Environmental barcoding: A next-generation sequencing approach for biomonitoring applications using river benthos

PLoS ONE

Volumn 6, Issue 4, 2011, Pages

  Hajibabaei, Mehrdad ^a   Shokralla, Shadi ^a   Zhou, Xin ^a   Singer, Gregory A C ^a   Baird, Donald J ^b  

^a UNIVERSITY OF GUELPH   (Canada)

^b UNIVERSITY OF NEW BRUNSWICK   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BENTHOS; BIODIVERSITY; BIOLOGICAL MONITORING; DNA BARCODING; DNA DETERMINATION; DNA SEQUENCE; ENVIRONMENTAL MONITORING; ENVIRONMENTAL PROTECTION; FEASIBILITY STUDY; FRESHWATER ENVIRONMENT; MACROINVERTEBRATE; MORPHOLOGY; NONHUMAN; PYROSEQUENCING; RIVER; SPECIES IDENTIFICATION; URBAN AREA; ANIMAL; CLASSIFICATION; GENETICS; INFORMATION PROCESSING; INVERTEBRATE; METHODOLOGY;

DNA; FRESH WATER;

ANIMALS; AUTOMATIC DATA PROCESSING; BIODIVERSITY; DNA; ENVIRONMENTAL MONITORING; FRESH WATER; INVERTEBRATES;

EID: 79954587407     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0017497     Document Type: Article

References (25)

1. Chapman AD, (2009) Numbers of Living Species in Australia and the World: A Report for the Australian Biological Resources Study. Toowoomba.
2. Wilson EO, (1985) Time to Revive Systematics. Science 230: 1227.
3. Sanger F, Nicklen S, Coulson AR, (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74: 5463-5467.
4. Hebert PDN, Cywinska A, Ball SL, deWaard JR, (2003) Biological identifications through DNA barcodes. Proc R Soc Lond B Biol Sci 270: 313-321.
5. Marshall E, (2005) Taxonomy. Will DNA bar codes breathe life into classification? Science 307: 1037.
6. Savolainen V, Cowan RS, Vogler AP, Roderick GK, Lane R, (2005) Towards writing the encyclopaedia of life: an introduction to DNA barcoding. Philos Trans R Soc Lond B Biol Sci 360: 1805-1811.
7. Hajibabaei M, Singer GAC, Hebert PDN, Hickey DA, (2007) DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends Genet 23: 167-172.
8. Ratnasingham S, Hebert PDN, (2007) BOLD: The Barcode of Life Data System (www.barcodinglife.org). Mol Ecol Notes 7: 355-364.
9. deWaard JR, Ivanova NV, Hajibabaei M, Hebert PDN, (2008) Assembling DNA barcodes. Analytical protocols. Methods Mol Biol 410: 275-293.
10. Hajibabaei M, dewaard JR, Ivanova NV, Ratnasingham S, Dooh RT, et al. (2005) Critical factors for assembling a high volume of DNA barcodes. Philos Trans R Soc Lond B Biol Sci 360: 1959-1967.
11. Hajibabaei M, Smith MA, Janzen DH, Rodriguez JJ, Whitfield JB, et al. (2006) A minimalist barcode can identify a specimen whose DNA is degraded. Mol Ecol Notes 6: 959-964.
12. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
13. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, et al. (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A 103: 12115-12120.
14. Meusnier I, Singer GA, Landry JF, Hickey DA, Hebert PDN, et al. (2008) A universal DNA mini-barcode for biodiversity analysis. BMC Genomics 9: 214.
15. Ley RE, Turnbaugh PJ, Klein S, Gordon JI, (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444: 1022-1023.
16. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
17. Hajibabaei M, Singer GA, Clare EL, Hebert PDN, (2007) Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring. BMC Biol 5: 24.
18. Simen BB, Simons JF, Hullsiek KH, Novak RM, Macarthur RD, et al. (2009) Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. J Infect Dis 199: 693-701.
19. Shokralla S, Singer GA, Hajibabaei M, (2010) Direct PCR amplification and sequencing of specimens' DNA from preservative ethanol. Biotechniques 48: 233-234.
20. Creer S, Fonseca VG, Porazinska DL, Giblin-Davis RM, Sung W, et al. (2010) Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises. Mol Ecol 19 (Suppl 1): 4-20.
21. Hajibabaei M, Singer GA, (2009) Googling DNA sequences on the World Wide Web. BMC Bioinformatics 10 (Suppl 14): S4.
22. Singer GA, Hajibabaei M, (2009) iBarcode.org: web-based molecular biodiversity analysis. BMC Bioinformatics 10 (Suppl 6): S14.
23. Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W, (2004) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc Natl Acad Sci U S A 101: 14812-14817.
24. 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. Mol Mar Biol Biotechnol 3: 294-299.
25. Tamura K, Dudley J, Nei M, Kumar S, (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.