Advancing nematode barcoding: A primer cocktail for the cytochrome c oxidase subunit I gene from vertebrate parasitic nematodes

Molecular Ecology Resources

Volumn 13, Issue 6, 2013, Pages 1108-1115

  Prosser, Sean W J ^a   Velarde Aguilar, Maria G ^b   León Règagnon, Virginia ^b   Hebert, Paul D N ^a  

^a UNIVERSITY OF GUELPH   (Canada)

^b UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

Author keywords

Barcoding; Identification; Nematodes; Primers

Indexed keywords

CYTOCHROME C OXIDASE;

ANIMAL; ARTICLE; BARCODING; CHEMISTRY; CLASSIFICATION; DNA BARCODING; GENETICS; HIGH THROUGHPUT SEQUENCING; IDENTIFICATION; METHODOLOGY; MOLECULAR GENETICS; NEMATODE; NUCLEOTIDE SEQUENCE; PARASITOLOGY; PHYLOGENY; PRIMERS; VERTEBRATE;

BARCODING; IDENTIFICATION; NEMATODES; PRIMERS;

ANIMALS; DNA BARCODING, TAXONOMIC; ELECTRON TRANSPORT COMPLEX IV; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE DATA; NEMATODA; PHYLOGENY; VERTEBRATES;

EID: 84885446102     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12082     Document Type: Article

References (55)

1. Anderson RC (2000) Nematode Parasites of Vertebrates: Their Development and Transmission, 2nd edn. CABI Publishing, Oxford, UK.
2. Asbakk K, Aars J, Derocher AE et al. (2010) Serosurvey for Trichinella in polar bears (Ursus maritimus) from Svalbard and the Barents Sea. Veterinary Parasitology, 172, 256-263.
3. Barr MM (2005) Caenorhabditis elegans as a model to study renal development and disease: sexy cilia. Journal of the American Society of Nephrology, 16, 305-312.
4. Blaxter M (2003) Counting angels with DNA. Nature, 421, 122-124.
5. Blaxter ML, De Ley P, Garey JR et al. (1998) A molecular evolutionary framework for the phylum Nematoda. Nature, 392, 71-75.
6. Brown M, Cronk B, DeSinner F, Green JE, Gibbons JE, Kuitunen-Ekbaum E (1949) A note on trichinosis in animals of the Canadian Northwest Territories. Canadian Journal of Public Health, 40, 20-21.
7. Brown M, Green JE, Boag TJ, Kuitunen-Ekbaum E (1950) Parasitic infections in the Eskimos at Igloolik, N.W.T. Canadian Journal of Public Health, 41, 508-512.
8. Campagna L, Lijtmaer DA, Kerr KCR et al. (2010) DNA barcodes provide new evidence of a recent radiation in the genus Sporophila (Aves: Passeriformes). Molecular Ecology Resources, 10, 449-458.
9. Clare EL, Lim BK, Fenton MB, Hebert PDN (2011) Neotropical bats: estimating species diversity with DNA barcodes. PLoS ONE, 6, e22648.
10. Clarke DJ (2008) Photorhabdus: a model for the analysis of pathogenicity and mutualism. Cellular Microbiology, 10, 2159-2167.
11. Coomans A (2000) Nematode systematics: past, present and future. Nematology, 2, 3-7.
12. Coomans A (2002) Present status and future of nematode systematics. Nematology, 4, 573-582.
13. Creer S, Fonseca VG, Porazinska DI et al. (2010) Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises. Molecular Ecology, 19(Suppl. 1), 4-20.
14. Dailey MD (2009) A new species of Parafilaroides (Nematoda: Filaroididae) in three species of fur seals (Carnivora: Otariidae) from the southern hemisphere. Journal of Parasitology, 95, 156-159.
15. De Ley P (2006) A quick tour of nematode diversity and the backbone of nematode phylogeny. WormBook: the online review of C. elegans biology, 25, 1-8.
16. De Ley P, De Ley IT, Morris K et al. (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 Sciences, 360, 1945-1958.
17. Denver DR, Clark KA, Raboin MJ (2011) Reproductive mode evolution in nematodes: insights from molecular phylogenies and recently discovered species. Molecular Phylogenetics and Evolution, 61, 584-592.
18. Derycke S, Fonseca G, Vierstraete A, Van-Fleuteren J, Vincx M, Moens T (2008) Disentangling taxonomy within the Rhabditis (Pellioditis) marina (Nematoda, Rhabditidae) species complex using molecular and morphological tools. Zoological Journal of the Linnaean Society, 152, 1-15.
19. Derycke S, Vanaverbeke J, Rigaux A, Backeljau T, Moens T (2010) Exploring the use of cytochrome oxidase c subunit 1 (COI) for DNA barcoding of free-living marine nematodes. PLoS ONE, 5, e13716.
20. Ekschmitt K, Korthals GW (2006) Nematodes as sentinels of heavy metals and organic toxicants in the soil. Journal of Nematology, 38, 13-19.
21. Elsasser SC, Floyd R, Hebert PDN, Schulte-Hostedde AI (2009) Species identification of North American guinea worms (Nematoda: Dracunculus) with DNA barcoding. Molecular Ecology Resources, 9, 707-712.
22. Ferri E, Barbuto M, Bain O et al. (2009) Integrated taxonomy: traditional approach and DNA barcoding for the identification of filarioid worms and related parasites (Nematoda). Frontiers in Zoology, 6, 1-12.
23. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature, 391, 806-811.
24. Floyd R, Abebe E, Papert A, Blaxter M (2002) Molecular barcodes for soil nematode identification. Molecular Ecology, 11, 839-850.
25. 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.
26. Godfray HCJ (2002) Challenges for taxonomy. Nature, 417, 17-19.
27. Hajibabaei M, DeWaard JR, Ivanova NV et al. (2005) Critical factors for assembling a high volume of DNA barcodes. Philosophical Transactions of the Royal Society B-Biological Sciences, 360, 1959-1967.
28. Hebert PDN, Cywinska A, Ball SL, DeWaard JR (2003a) Biological identifications through DNA barcodes. Proceedings of the Royal Society of London Series B-Biological Sciences, 270, 313-321.
29. Hebert PDN, Ratnasingham S, DeWaard JR (2003b) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London Series B-Biological Sciences, 270, S96-S99.
30. Hodda M (2007) Phylum Nematoda In: Linnaeus Tercentenary: Progress in Invertebrate Taxonomy. (eds Zhang Z.-Q., Shear W. A.) Zootaxa 1668, 1-766.
31. Hodda M (2011) Phylum Nematoda Cobb 1932. In: Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness. (ed Zhang Z.-Q.) Zootaxa, 3148, 63-95.
32. Hodda M, Cook DC (2009) Economic impact from unrestricted spread of potato cyst nematodes in Australia. Phytopathology, 99, 1387-1393.
33. Hoess S, Claus E, Von der Ohe PC et al. (2011) Nematode species at risk - A metric to assess pollution in soft sediments of freshwaters. Environment International, 37, 940-949.
34. Hugot JP, Baujard P, Morand S (2001) Biodiversity in helminths and nematodes as a field of study: an overview. Nematology, 3, 199-208.
35. Ivanova NV, Dewaard JR, Hebert PDN (2006) An inexpensive, automation-friendly protocol for recovering high-quality DNA. Molecular Ecology Notes, 6, 998-1002.
36. Ivanova NV, Zemlak TS, Hanner RH, Hebert PDN (2007) Universal primer cocktails for fish DNA barcoding. Molecular Ecology Notes, 7, 544-548.
37. Jadiya P, Khan A, Sammi SR, Kaur S, Mir SS, Nazir A (2011) Anti-Parkinsonian effects of Bacopa monnieri: insights from transgenic and pharmacological Caenorhabditis elegans models of Parkinson's disease. Biochemical and Biophysical Research Communications, 413, 605-610.
38. Kumar NP, Srinivasan R, Jambulingam P (2012) DNA barcoding for identification of sand flies (Diptera: Psychodidae) in India. Molecular Ecology Resources, 12, 414-420.
39. Larkin MA, Blackshields G, Brown NP et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.
40. Manguin S, Bangs MJ, Pothikasikorn J, Chareonviriyaphap T (2010) Review on global co-transmission of human Plasmodium species and Wuchereria bancrofti by Anopheles mosquitoes. Infection Genetics and Evolution, 10, 159-177.
41. Marcogliese D (2005) Parasites of the superorganism: are they indicators of ecosystem health? International Journal of Parasitology, 35, 705-716.
42. Martínez-Salazar EA (2008) Sistemática y biogeografía del género Rhabdias Stiles y Hassall, 1905 (Nematoda: Rhabdiasidae) en México. Tesis DoctoradoPosgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, 495pp.
43. Messing J (1993) M13 cloning vehicles: their contribution to DNA sequencing. Methods in Molecular Biology, 23, 9-22.
44. Nadler SA (2002) Species delimitation and nematode biodiversity: phylogenies rule. Nematology, 4, 615-625.
45. Ott JA, Novak R, Schiemer F, Hentschel U, Nebelsick M, Polz M (1991) Tackling the sulfide gradient: a novel strategy involving marine nematodes and chemoautotrophic ectosymbionts. Marine Ecology, 12, 261-279.
46. Palm HW, Kleinertz S, Ruckert S (2011) Parasite diversity as an indicator of environmental change? An example from tropical grouper (Epinephelus fuscoguttatus) mariculture in Indonesia. Parasitology, 138, 1793-1803.
47. Powers T, Harris T, Higgins R, Mullin P, Sutton L, Powers K (2011) MOTUs, morphology, and biodiversity estimation: a case study using nemtodes of the suborder criconematina and a conserved 18S DNA barcode. Journal of Nematology, 43, 35-48.
48. Sambongi Y, Nagae T, Liu Y et al. (1999) Sensing of cadmium and copper ions by externally exposed ADL, ASE, and ASH neurons elicits avoidance response in Caenorhabditis elegans. NeuroReport, 10, 753-757.
49. Siddal ME, Kivst S, Phillips A, Oceguera-Figueroa A (2012) DNA barcoding of parasitic nematodes: is it Kosher? Journal of Parasitology, 98, 692-694.
50. Subbotin SA, Ragsdale EJ, Mullens T, Roberts PA, Mundo-Ocampo M, Baldwin JG (2008) A phylogenetic framework for root lesion nematodes of the genus Pratylenchus (Nematoda): evidence from 18S and D2-D3 expansion segments of 28S ribosomal RNA genes and morphological characters. Molecular Phylogenetics and Evolution, 48, 491-505.
51. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731-2739.
52. Vanreusel A, De Groote A, Gollner S, Bright M (2010) Ecology and biogeography of free-living nematodes associated with chemosynthetic environments in the deep sea: a review. PLoS ONE, 5, e12449.
53. Weigt LA, Baldwin CC, Driskell A, Smith DG, Ormos A, Reyier EA (2012) Using DNA barcoding to assess Caribbean reef fish biodiversity: expanding taxonomic and geographic coverage. PLoS ONE, 7, e41059.
54. Wijova M, Moravec F, Horak A, Modry D, Lukes J (2005) Phylogenetic position of Dracunculus medinensis and some related nematodes inferred from 18S rRNA. Parasitology Research, 96, 133-135.
55. Wu HC, Chen PC, Tsay TT (2010) Assessment of nematode community structure as a bioindicator in river monitoring. Environmental Pollution, 158, 1741-1747.