Linking operational clustered taxonomic units (OCTUs) from parallel ultra sequencing (PUS) to nematode species

Academic Article

Abstract

  • DNA-sequence-based approaches such as single nematode PCR and sequencing have been successfully used in nematode species diagnostics. Here, we use SSU rDNA sequences generated from an artificially-assembled community of nematodes of known identity and relative abundance to assess a relationship between nematode species and operationally clustered taxonomic units (OCTUs). OCTUs that formed at 95% similarity underestimated species richness by ca 30%, and all expected species were recovered only at 99% OCTU similarity. Although the number of OCTUs formed at 99% similarity was considerably higher than the actual number of nematode species, a pattern of the distribution of OCTUs within each species allowed an assignment of OCTUs to specific species. The pattern was highly predictable and helped to discern rather than obscure species recognition. The patterns and parameters that emerged from the control nematode dataset were then used to test our approach on environmental samples of nematodes obtained from a tropical rainforest in Costa Rica.
  • Authors

  • Porazinska, Dorota L
  • Giblin-Davis, Robin M
  • Sung, Way
  • Thomas, William
  • Status

    Publication Date

  • April 15, 2010
  • Has Subject Area

    Published In

  • Zootaxa  Journal
  • Keywords

  • DNA barcoding
  • biodiversity
  • high-throughput sequencing
  • metagenetic
  • nematode
  • Digital Object Identifier (doi)

    Start Page

  • 55
  • End Page

  • 63
  • Volume

  • 2427
  • Issue

  • 2427