98% sequence similarity) and an additional 32% could be assigned to a higher taxonomic level using Bayesian assignment.CONCLUSIONS: The molecular analysis of gut contents targeting the 313 COI fragment using the newly designed mlCOIintF primer in combination with the jgHCO2198 primer offers enormous promise for metazoan metabarcoding studies. We believe that this primer set will be a valuable asset for a range of applications from large-scale biodiversity assessments to food web studies." />
Display options
Cite
Leray M, Yang JY, Meyer CP, et al. 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. Front Zool. 2013;10:34doi: 10.1186/1742-9994-10-34.
Leray, M., Yang, J. Y., Meyer, C. P., Mills, S. C., Agudelo, N., Ranwez, V., Boehm, J. T., & Machida, R. J. (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, 1034. https://doi.org/10.1186/1742-9994-10-34
Leray, Matthieu, et al. "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 vol. 10 (2013): 34. doi: https://doi.org/10.1186/1742-9994-10-34
Leray M, Yang JY, Meyer CP, Mills SC, Agudelo N, Ranwez V, Boehm JT, Machida RJ. 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. Front Zool. 2013 Jun 14;10:34. doi: 10.1186/1742-9994-10-34. eCollection 2013. PMID: 23767809; PMCID: PMC3686579.
Copy Download .nbib Format: NLM
Share it on

Front Zool. 2013 Jun 14;10:34. doi: 10.1186/1742-9994-10-34. eCollection 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

Matthieu Leray, Joy Y Yang, Christopher P Meyer, Suzanne C Mills, Natalia Agudelo, Vincent Ranwez, Joel T Boehm, Ryuji J Machida

Affiliations

  1. Laboratoire d'Excellence "CORAIL", USR 3278 CRIOBE CNRS-EPHE, CBETM de l'Université de Perpignan, 66860, Perpignan Cedex, France ; Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, MRC-163, Washington, DC 20013-7012, USA.
  2. National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA.
  3. Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, MRC-163, Washington, DC 20013-7012, USA.
  4. Laboratoire d'Excellence "CORAIL", USR 3278 CRIOBE CNRS-EPHE, CBETM de l'Université de Perpignan, 66860, Perpignan Cedex, France.
  5. Montpellier SupAgro (UMR AGAP), Montpellier, France.
  6. Biology Department, City College of New York, New York, NY 10031, USA ; The Graduate Center, City University of New York, New York, NY 10016, USA.
  7. Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.

PMID: 23767809 PMCID: PMC3686579 DOI: 10.1186/1742-9994-10-34

Abstract

INTRODUCTION: The PCR-based analysis of homologous genes has become one of the most powerful approaches for species detection and identification, particularly with the recent availability of Next Generation Sequencing platforms (NGS) making it possible to identify species composition from a broad range of environmental samples. Identifying species from these samples relies on the ability to match sequences with reference barcodes for taxonomic identification. Unfortunately, most studies of environmental samples have targeted ribosomal markers, despite the fact that the mitochondrial Cytochrome c Oxidase subunit I gene (COI) is by far the most widely available sequence region in public reference libraries. This is largely because the available versatile ("universal") COI primers target the 658 barcoding region, whose size is considered too large for many NGS applications. Moreover, traditional barcoding primers are known to be poorly conserved across some taxonomic groups.

RESULTS: We first design a new PCR primer within the highly variable mitochondrial COI region, the "mlCOIintF" primer. We then show that this newly designed forward primer combined with the "jgHCO2198" reverse primer to target a 313 bp fragment performs well across metazoan diversity, with higher success rates than versatile primer sets traditionally used for DNA barcoding (i.e. LCO1490/HCO2198). Finally, we demonstrate how the shorter COI fragment coupled with an efficient bioinformatics pipeline can be used to characterize species diversity from environmental samples by pyrosequencing. We examine the gut contents of three species of planktivorous and benthivorous coral reef fish (family: Apogonidae and Holocentridae). After the removal of dubious COI sequences, we obtained a total of 334 prey Operational Taxonomic Units (OTUs) belonging to 14 phyla from 16 fish guts. Of these, 52.5% matched a reference barcode (>98% sequence similarity) and an additional 32% could be assigned to a higher taxonomic level using Bayesian assignment.

CONCLUSIONS: The molecular analysis of gut contents targeting the 313 COI fragment using the newly designed mlCOIintF primer in combination with the jgHCO2198 primer offers enormous promise for metazoan metabarcoding studies. We believe that this primer set will be a valuable asset for a range of applications from large-scale biodiversity assessments to food web studies.

Keywords: DNA barcoding; Food web; Mini-barcode; Mitochondrial marker; Second generation sequencing; Trophic interactions

References

  1. Mol Ecol Resour. 2010 Nov;10(6):960-7 - PubMed
  2. PLoS One. 2011;6(6):e21441 - PubMed
  3. PLoS One. 2012;7(4):e35887 - PubMed
  4. Mol Ecol. 2012 Apr;21(8):1931-50 - PubMed
  5. PLoS One. 2012;7(10):e47363 - PubMed
  6. Mol Ecol Resour. 2009 Jan;9(1):51-60 - PubMed
  7. Genome. 2003 Feb;46(1):48-50 - PubMed
  8. Environ Microbiol. 2009 May;11(5):1292-302 - PubMed
  9. ISME J. 2010 May;4(5):642-7 - PubMed
  10. Mol Ecol. 2002 Dec;11(12):2679-90 - PubMed
  11. Syst Biol. 2008 Oct;57(5):750-7 - PubMed
  12. PLoS One. 2010 Apr 28;5(4):e10278 - PubMed
  13. Mol Ecol Resour. 2012 Jan;12(1):5-17 - PubMed
  14. PLoS One. 2012;7(4):e35456 - PubMed
  15. Mol Ecol. 2011 Apr;20(8):1772-80 - PubMed
  16. Appl Environ Microbiol. 2009 Dec;75(23):7537-41 - PubMed
  17. BMC Genomics. 2010 Jul 16;11:434 - PubMed
  18. Mol Ecol. 2004 May;13(5):1313-22 - PubMed
  19. Philos Trans R Soc Lond B Biol Sci. 2005 Oct 29;360(1462):1917-24 - PubMed
  20. Front Zool. 2006 Aug 16;3:11 - PubMed
  21. Nat Commun. 2010 Oct 19;1:98 - PubMed
  22. Syst Biol. 2009 Aug;58(4):445-51 - PubMed
  23. Proc Biol Sci. 2003 Feb 7;270(1512):313-21 - PubMed
  24. BMC Bioinformatics. 2011 Jan 28;12:38 - PubMed
  25. Am Nat. 2003 Jan;161(1):1-28 - PubMed
  26. Mol Ecol Resour. 2013 Sep;13(5):851-61 - PubMed
  27. PLoS One. 2011;6(9):e22594 - PubMed
  28. BMC Genomics. 2008 May 12;9:214 - PubMed
  29. PLoS One. 2012;7(2):e32104 - PubMed
  30. PLoS One. 2011;6(10):e25776 - PubMed
  31. Mol Ecol. 2009 May;18(9):2022-38 - PubMed
  32. Mol Ecol. 2010 Mar;19 Suppl 1:4-20 - PubMed
  33. BMC Genomics. 2009 Sep 17;10:438 - PubMed
  34. Mol Ecol Resour. 2011 Sep;11(5):759-69 - PubMed
  35. Bioinformatics. 2011 Mar 1;27(5):611-8 - PubMed
  36. Mol Ecol. 2012 Apr;21(8):2045-50 - PubMed
  37. Mol Mar Biol Biotechnol. 1994 Oct;3(5):294-9 - PubMed
  38. PLoS One. 2012;7(9):e46180 - PubMed
  39. Front Zool. 2009 Aug 20;6:16 - PubMed
  40. Front Zool. 2008 Jul 20;5:12 - PubMed
  41. J Mol Biol. 1990 Oct 5;215(3):403-10 - PubMed
  42. PLoS One. 2013 Apr 08;8(4):e58076 - PubMed
  43. Q Rev Biol. 1991 Dec;66(4):411-53 - PubMed
  44. Bioinformatics. 2011 Aug 15;27(16):2194-200 - PubMed
  45. PLoS One. 2010 Oct 28;5(10):e13716 - PubMed

Publication Types