Development and evaluation of a DNA-barcoding approach for the rapid identification of nematodes

Bhadury, Punyasloke; Austen, Melanie C.; Bilton, David T.; Lambshead, P. J. D.; Rogers, Alex D.; Smerdon, Gary R.

doi:10.3354/meps320001

Cited by 139 publications

(129 citation statements)

References 20 publications

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“…this gene, however, is difficult to amplify successfully for several animal species (Bhadury et al 2006, Moszczynska et al 2009, Hoareau and Boissin 2010, including species of Gyrodactylus (see Meinilä et al 2002, this study). Alternatively, the coii gene has been successfully used as a molecular marker in phylogenetic reconstructions and evolutionary studies for various species of animals (spicer 1995, Adkins et al 1996, Frati et al 1997, caterino and sperling 1999, Pruess et al 2000, Piaggio and spicer 2001, rawson and Burton 2006.…”

Section: Discussionmentioning

confidence: 99%

Neotropical Monogenoidea. 58. Three new species of Gyrodactylus (Gyrodactylidae) from Scleromystax spp. (Callichthyidae) and the proposal of COII gene as an additional fragment for barcoding gyrodactylids

Bueno‐Silva¹,

Boeger²

2014

FOLIA PARASIT

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Section: Discussionmentioning

confidence: 99%

Neotropical Monogenoidea. 58. Three new species of Gyrodactylus (Gyrodactylidae) from Scleromystax spp. (Callichthyidae) and the proposal of COII gene as an additional fragment for barcoding gyrodactylids

Bueno‐Silva¹,

Boeger²

2014

FOLIA PARASIT

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“…67 % in Pereira et al 2010). Earlier studies using the same fragment reported ''unreliable'' amplification results (Bhadury et al 2006a) as well as very high success rates (De Ley et al 2005). Due to the fact that a marker for molecular species identification should be easy to amplify, PCR optimization represents an essential task for further studies.…”

Section: Choice Of Marker and Implicationsmentioning

confidence: 99%

The application of DNA sequence data for the identification of benthic nematodes from the North Sea

2014

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Nematodes or roundworms represent one of the most diverse and dominant taxon in marine benthic habitats. Whereas a morphological identification of many species is challenging, the application of molecular markers represents a promising approach for species discrimination and identification. In this study, we used an integrative taxonomic approach, combining both molecular and morphological methods, to characterize nematodes of distinct sex and ontogenetic stages from three sampling sites of the North Sea. Morphospecies were discriminated after first visual determination, followed by a molecular analysis of the nuclear 28S rDNA: D2-D3 marker. By linking each sequence to a morphological voucher, discordant morphological identification was subjected to a so-called reverse taxonomic approach. Molecular operational taxonomic units (MOTUs) and morphospecies were compared for all of the three sampling sites to assess concordance of methodology. In total, 32 MOTUs and 26 morphospecies were assigned, of which 12 taxa were identified as described species. Both approaches showed high concordance in taxon assignment (84.4 %) except for a cluster comprising various Sabatieria species. Our study revealed the high potential of the analyzed fragment as a useful molecular marker for the identification of the North Sea nematodes and highlighted the applicability of this combined taxonomic approach in general.

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“…The availability of both conserved and variable regions, allowing the design of universal primers for subsequent amplification of variable regions of the 18S gene, make it a widely used marker for species identification purposes, such as DNA barcoding projects (e.g. Floyd et al 2002, Bhadury et al 2006. Finally, the existence of databases of ribosomal sequences (e.g.…”

Section: Relevance Of the 18s Rrna-targeted Probes For Species Identimentioning

confidence: 99%

In situ hybridization on whole larvae: a novel method for monitoring bivalve larvae

Goff-Vitry¹,

Chipman²,

Comtet³

2007

Mar. Ecol. Prog. Ser.

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Accurate and efficient identification to the species level of early larval stages has long been a problematic step in the study of marine invertebrates, due to the extremely small size of the larvae and their lack of diagnostic morphological characters. It is nonetheless, a prerequisite for any ecological study. As a consequence, a number of molecular approaches, mostly based on the PCR technique, have been developed over the last decade. We developed a method relying on specific rRNA-targeted oligonucleotide probes for in situ molecular hybridization using whole larvae. A colorimetric reaction following the hybridization allows signal detection with a light microscope. A total of 9 probes have been developed, targeting the species that are major components of benthic communities in several European bays. The method can be applied to roughly sorted wild plankton samples, and some steps could be automated. It is relatively inexpensive to implement and does not require costly equipment or expensive staff training. The overall larval morphology is preserved, allowing visual inspection. The quantitative aspect of the approach is another asset. Field-based studies of larval distribution and behaviour are possible applications of the method, as large numbers of samples can be screened to meet the requirements of adequate spatial and temporal coverage. It is also relevant for routine monitoring of target species, such as species of commercial interest, bio-indicators or invasive species.

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Development and evaluation of a DNA-barcoding approach for the rapid identification of nematodes

Cited by 139 publications

References 20 publications

Neotropical Monogenoidea. 58. Three new species of Gyrodactylus (Gyrodactylidae) from Scleromystax spp. (Callichthyidae) and the proposal of COII gene as an additional fragment for barcoding gyrodactylids

Neotropical Monogenoidea. 58. Three new species of Gyrodactylus (Gyrodactylidae) from Scleromystax spp. (Callichthyidae) and the proposal of COII gene as an additional fragment for barcoding gyrodactylids

The application of DNA sequence data for the identification of benthic nematodes from the North Sea

In situ hybridization on whole larvae: a novel method for monitoring bivalve larvae

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