Dutch DNA barcode users

Cases of DNA barcoding already being applied in NL, both in academia and in, for instance, regulatory control agencies such as PD are:

QBOL: Development of a new diagnostic tool using dna barcoding to identify quarantine organisms in support of plant health

Development of accurate identification tools for plant pathogens and pests is vital to support European Plant Health Policies. For this project Council Directive 2000/29/EC is important, listing some 275 organisms for which protective measures against introduction into and their spread within the Community needs to be taken. Those threats are now greater than ever because of the increases in the volumes, commodity types and origins of trade, the introduction of new crops, the continued expansion of the EU and the impact of climate change.

Currently identifying pathogens (in particular new emerging diseases) requires a staff with specialised skills in all disciplines (mycology, bacteriology, etc.); which is only possible within big centralised laboratory facilities. Taxonomy, phytopathology and other fields which are vital for sustaining sound public policy on phytosanitary issues are threatened with extinction.

Modern molecular identification/detection techniques may tackle the decline in skills since they often require much less specialist skills to perform, are more amenable for routine purposes and can be used for a whole range of different target organisms. Recently DNA barcoding has arisen as a robust and standardised approach to species identification. QBOL wants now to make DNA barcoding available for plant health diagnostics and to focus on strengthening the link between traditional and molecular taxonomy as a sustainable diagnostic resource.

Within QBOL collections harbouring plantpathogenic Q-organisms will be made available. Informative genes from selected species on the EU Directive and EPPO lists will be DNA barcoded from vouchered specimens. The sequences, together with taxonomic features, will be included in a new internet-based database system. A validation procedure on developed protocols and the database will be undertaken across worldwide partners to ensure robustness of procedures for use in a distributed network of laboratories across Europe.

Identifying fern gametophytes emerging from soil samples taken in the field. field. Arjen de Groot Plant Ecology & Biodiversity Group, Utrecht University

WODAN: investigating the colonization of planted forests in the Dutch Ijsselmeer polders by different plant groups. As a PhD-student within this project, Arjen de Groot studies the composition of soil diaspore banks of several forests, as well as of the lake bottom sediment of the IJsselmeer, from soil samples. When sporophytes are produced, these can normally be identified quite well. However, since successful fertilization of fern gametophytes is often limited, this may result in an unrealistically short list of found species in which self-fertilizing species might be overrepresented. Therefore DNA barcoding is applied in order to identify a subsample of the emerged gametophytes up to the lowest level possible (preferably) species level. Per individual, sequences of several regions of the ferns’ chloroplast genome are obtained and compared with online records (BLAST, BOLD), as well as analyzed phylogenetically using a self-produced database of reference sequences for most Dutch fern species, supplemented with Genbank records. First results, based on rbcL data, already look promising. Additional plastid regions (trnL-F, matK, psbA-trnH) will be sequenced and added to the analysis in order to increase its resolution to species level.

Identifcation of immature stages of Cymothoe (Nymphalidae) feeding on Rinorea (Violaceae) in Tropical Africa. Robin van Velzen Nationaal Herbarium Nederland (NHN) – Wageningen Branch & Biosystematics Group, Wageningen University

Identifying factors driving patterns of association between phytophagous insects and their host plants is one of the main themes in the field of insect-plant interactions. Robin van Velzen is working as a PhD student on a project that considers evolution of host plant associations of Cymothoe butterflies feeding on Rinorea. This strictly Afrotropical phytophagous system is unique within current knowledge of Nymphalidae host plant relationships because of its high level of specificity and the large number of congeneric species involved. The research aims at using a comparative phylogenetic, experimental approach by combining insect and host-plant phylogenetic trees with data from host-plant phytochemistry and behavioural experiments.
Quick and reliable identification of Cymothoe eggs and caterpillars found on Rinorea is imperative for this project. Because DNA barcoding can replace the time consuming practice of breeding immature stages for identification based on adult morphology, this technique is an important part of the project. Currently, a Cymothoe DNA barcode library is being built in collaboration with the Canadian Centre for DNA Barcoding (CCDB) and a network of specialist collectors of African butterflies. In addition to providing an efficient tool for identification, the DNA barcode library can also facilitate in tackling taxonomic problems and the discovery of cryptic species (van Velzen et al. 2007).

Robin van Velzen, Freek T. Bakker & Joop J.A. van Loon (2007) DNA barcoding reveals hidden species diversity in Cymothoe (Nymphalidae). Proc. Neth. Entomol. Soc. Meet. vol 18: 95-103

Versterking Infrastruktuur Plantengezondheid, coordinated by the Dutch Plant Protection Service/Plantenziektenkundige Dienst.

Efforts are ongoing to contribute to DNA barcoding the top three insect pests in The Netherlands: Tephritidae (true fruit flies), Spodoptera (army worm moths) and Bemisia (white fly). For each of these groups several or single species are targeted within broadest possible phylogenetic context, with a view to develop (sub)species-level identification assays. Contact Freek Bakker.

In addition, DNA barcoding is applied to invasive plants in The Netherlands, focussing on species causing economic damage (e.g. Cyperus esculentus in agriculture, blocking of waterways through rampant growth of Hydrocotyle ranunculoides), or causing problems in relation to health (e.g. allergic reaction of the skin when in contact with Heracleum mantegazzianum). The Dutch Ministry of Agriculture, Nature and Food Quality (LNV) has allowed the Consortium Invasive Plant Species a grant to build in four years time an information system for potentially invasive exotic plant species. The consortium can be contacted through Leni Duistermaat at the Nationaal Herbarium Nederland, Leiden University branch.

Dutch DNA barcode users

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