European Ocean Biodiversity Information System
[ report an error in this record ]basket (0): add | show Print this page
Exploring the use of cytochrome oxidase c Subunit 1 (COI) for DNA barcoding of free-living marine nematodes
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(10): e13716. dx.doi.org/10.1371/journal.pone.0013716
In: PLoS One. Public Library of Science: San Francisco. ISSN 1932-6203; e-ISSN 1932-6203
Peer reviewed article  
Available in  Authors 
    Vlaams Instituut voor de Zee: Open access 216874 [ download pdf ]
Keywords
    ANE, Netherlands, Westerschelde
    Enzymes > Coenzymes > Cytochromes
    Identification
    Nematoda [WoRMS]
    ANE, Belgium, Nieuwpoort [Marine Regions]; ANE, Netherlands, Westerschelde [Marine Regions]
    Marine/Coastal
Authors  Top 
  • Derycke, S.
  • Vanaverbeke, J.
  • Rigaux, A.
  • Backeljau, T.
  • Moens, T.
Abstract
    BackgroundThe identification of free-living marine nematodes is difficult because of the paucity of easily scorable diagnostic morphological characters. Consequently, molecular identification tools could solve this problem. Unfortunately, hitherto most of these tools relied on 18S rDNA and 28S rDNA sequences, which often lack sufficient resolution at the species level. In contrast, only a few mitochondrial COI data are available for free-living marine nematodes. Therefore, we investigate the amplification and sequencing success of two partitions of the COI gene, the M1-M6 barcoding region and the I3-M11 partition.MethodologyBoth partitions were analysed in 41 nematode species from a wide phylogenetic range. The taxon specific primers for the I3-M11 partition outperformed the universal M1-M6 primers in terms of amplification success (87.8% vs. 65.8%, respectively) and produced a higher number of bidirectional COI sequences (65.8% vs 39.0%, respectively). A threshold value of 5% K2P genetic divergence marked a clear DNA barcoding gap separating intra- and interspecific distances: 99.3% of all interspecific comparisons were >0.05, while 99.5% of all intraspecific comparisons were <0.05 K2P distance.ConclusionThe I3-M11 partition reliably identifies a wide range of marine nematodes, and our data show the need for a strict scrutiny of the obtained sequences, since contamination, nuclear pseudogenes and endosymbionts may confuse nematode species identification by COI sequences
All data in the Integrated Marine Information System (IMIS) is subject to the VLIZ privacy policy Top | Authors