Barcoding marine nematodes: An improved set of nematode 18S rRNA primers to overcome eukaryotic co-interference

Hydrobiologia

Volumn 641, Issue 1, 2010, Pages 245-251

  Bhadury, Punyasloke ^a   Austen, Melanie C ^b  

^a BIDHAN CHANDRA KRISHI VISWAVIDYALAYA   (India)

^b PLYMOUTH MARINE LABORATORY   (United Kingdom)

Author keywords

18S rRNA primers; DNA barcoding; Eukaryotic co interference; Marine nematodes

Indexed keywords

18S RRNA; AMPLICONS; BIOMONITORING; COMMUNITY COMPOSITION; DNA BARCODING; GENBANK; INTERTIDAL SEDIMENTS; MARINE ECOSYSTEM; MOLECULAR DATABASE; NEMATODE COMMUNITIES; NEW JERSEY;

BIODIVERSITY; DATABASE SYSTEMS; DNA; ECOSYSTEMS; GENES; LANDFORMS; RNA; SEDIMENTOLOGY;

DNA SEQUENCES;

COASTAL SEDIMENT; DATABASE; DNA; EUKARYOTE; INTERFERENCE COMPETITION; INTERTIDAL ENVIRONMENT; MARINE ECOSYSTEM; NEMATODE; RNA; SPECIES DIVERSITY; ZOOBENTHOS; ZOOGEOGRAPHICAL REGION;

NEW JERSEY; UNITED STATES;

DAPTONEMA; EUKARYOTA; METACHROMADORA; NEMATODA;

EID: 76349124053     PISSN: 00188158     EISSN: 15735117     Source Type: Journal    
DOI: 10.1007/s10750-009-0088-z     Document Type: Article

References (21)

1. Austen, M. C., 2004. Natural nematode communities are useful tools to address ecological and applied questions. Nematology Monographs and Perspectives 2: 1-17.
2. Austen, M. C. & A. J. McEvoy, 1997. The use of offshore meiobenthic communities in laboratory microcosm experiments: response to heavy metal contamination. Journal of Experimental Marine Biology and Ecology 211: 247-261.
3. Bhadury, P., M. C. Austen, D. T. Bilton, P. J. D. Lambshead, A. D. Rogers & G. R. Smerdon, 2006a. Development and evaluation of a DNA-barcoding approach for the rapid identification of nematodes. Marine Ecology Progress Series 320: 1-9.
4. Bhadury, P., M. C. Austen, D. T. Bilton, P. J. D. Lambshead, A. D. Rogers & G. R. Smerdon, 2006b. Molecular detection of marine nematodes from environmental samples: overcoming eukaryotic interference. Aquatic Microbial Ecology 44: 97-103.
5. Bhadury, P., M. C. Austen, D. T. Bilton, P. J. D. Lambshead, A. D. Rogers & G. R. Smerdon, 2007. Exploitation of archived marine nematodes-a hot lysis DNA extraction protocol for molecular studies. Zool Scripta 36: 93-98.
6. Bhadury, P., M. C. Austen, D. T. Bilton, P. J. D. Lambshead, A. D. Rogers & G. R. Smerdon, 2008. Evaluation of combined morphological and molecular techniques for marine nematode (Terschellingia spp.) identification. Marine Biology 154: 509-518.
7. Blaxter, M. L., P. De Ley, J. R. Garey, L. X. Liu, P. Scheldeman, A. Vierstraete, J. R. Vanfleteren, L. Y. Mackey, M. Dorris, L. M. Frisse, J. T. Vida & V. K. Thomas, 1998. A molecular evolutionary framework for the phylum Nematoda. Nature 392: 71-75.
8. Boyd, S. E., H. L. Rees & C. A. Richardson, 2000. Nematodes as sensitive indicators of changes at dredged material disposal sites. Estuarine Coastal and Shelf Science 51: 805-819.
9. Cook, A. A., P. Bhadury, N. J. Debenham, B. H. M. Meldal, M. L. Blaxter, G. R. Smerdon, M. C. Austen, P. J. D. Lambshead & A. D. Rogers, 2005. Denaturing gradient gel electrophoresis (DGGE) as a tool for identification of marine nematodes. Marine Ecology Progress Series 291: 103-113.
10. De Ley, P., I. T. De Ley, K. Morris, E. Abebe, M. Mundo, M. Yoder, J. Heras, D. Waumann, A. Rocha-Olivares, J. Burr, J. G. Baldwin & W. K. Thomas, 2005. An integrated approach to fast and informative morphological vouchering of nematodes for applications in molecular barcoding. Philosophical Transactions of the Royal Society B Biological Science 360: 1945-1958.
11. Derycke, S., T. Backeljau, C. Vlaeminck, A. Vierstraete, J. Vanfleteren, M. Vincx & T. Moens, 2007. Spatiotemporal analysis of population genetic structure in Geomonhystera disjuncta (Nematoda, Monhysteridae) reveals high levels of molecular diversity. Marine Biology 151: 1799-1812.
12. Feazel, L. M., J. R. Spear, A. B. Berger, J. K. Harris, D. N. Frank, R. E. Ley & N. R. Pace, 2008. Eucaryotic diversity in a hypersaline microbial mat. Applied and Environmental Microbiology 74: 329-332.
13. Floyd, R. M., A. D. Rogers, P. J. D. Lambshead & C. R. Smith, 2005. Nematode-specific PCR primers for the 18S small subunit ribosomal RNA gene. Molecular Ecology Notes 5: 611-612.
14. Foucher, A. & M. Wilson, 2002. Development of a polymerase chain reaction-based denaturing gradient gel electrophoresis technique to study nematode species biodiversity using the 18S rDNA gene. Molecular Ecology Notes 2: 45-48.
15. Jeanmougin, F., J. D. Thompson, M. Gouy, D. G. Higgins & T. J. Gibson, 1998. Multiple sequence alignment with Clustal X. Trends in Biochemical Sciences 23: 403-405.
16. Kumar, S., K. Tamura & M. Nei, 2004. MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings in Bioinformatics 5: 150-163.
17. Lambshead, P. J. D., 1986. Sub-catastrophic sewage and industrial waste contamination as revealed by marine nematode faunal analysis. Marine Ecology Progress Series 29: 247-260.
18. Meldal, B. H. M., N. J. Debenham, P. De Ley, et al., 2007. An improved molecular phylogeny of the Nematoda with special emphasis on marine nematode taxa. Molecular Phylogenetics and Evolution 42: 622-636.
19. Rozen, S. & H. Skaletsky, 2000. PRIMER 3 on the WWW for general users and for biologist programmers. In Krawetz, S. & S. Misener (eds), Bioinformatics: Methods and Protocols. Humana Press, Totowa, NJ: 365-368 (available on internet at http://Fokker. wi. mit. edu/primer3).
20. Steyart, M., N. Garner, D. van Gansbeke & M. Vincx, 1999. Nematode communities from the North Sea: environmental controls on species diversity and vertical distribution within the sediment. Journal of the Marine Biological Association of the United Kingdom 79: 253-264.
21. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin & D. G. Higgins, 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25: 4876-4882.