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Task 2.1.1. Production of the DNA database for the Arctic region

Task Lead: CO01 – CNRS Dr. Pierre Taberlet, Laboratoire d'Ecologie Alpine, Centre National de la Recherche Scientifique, Grenoble, France

This work pioneered the production of a database of DNA sequences that can be used to identify environmental plant DNA, that is, DNA retireved not from plants themselves but from the soil in which they are growing, or grew.  Plant-derived DNA is broken down in the soil environment but can be retrieved as short (~100 base-pair) strands; thus the approach differs from the production of conventional taxonomic molecular catalogues that rely upon sequences of many hundreds of base pairs.

A particular segment of chloroplast DNA (trnL UAA intron) was used. For three important plant families, Poaceae (grasses), Cyperaceae (sedges) and Asteraceae (aster family) we used a nuclear DNA sequence (ITS1), because the trnL approach failed to deliver adequate taxonomic resolution at genus and species level.  We used a quality control system in which partners CO01 and CR06 carried out blind replications of 10-20% of all the samples.  For vascular plants in the Arctic,  Ecochange work has created  a catalogue of so-called 'metabarcodes‘ for over 800 species (Sonstebø et al 2010); this has been augmented with metabarcodes for boreal zone vascular plant species by further  work at the University of Oslo. This work provides the foundation for identifying DNA retrieved from ancient soils and sediments.

Publications:
  • Sønstebø J.H., Gielly L., Brysting A.K., Elven R., Edwards M., Haile J., Willerslev E., Coissac E., Rioux D., Sannier J., Taberlet P. & Brochmann C. (2010). Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate. Molecular Ecology Resources, 10, 1009-1018

For information on the modelcular methods see also:

  • Taberlet P., Coissac E., Pompanon F., Gielly L., Miquel C., Valentini A., Vermat T., Corthier G., Brochmann C. & Willerslev E. (2007). Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Research, 35, 8
  • Valentini, A. F. Pompanon and P. Taberlet. 2008. DNA barcoding for ecologists rends in Ecology and Evolution Vol.24 No.2 110-117[doi:10.1016/j.tree.2008.09.011]

 

 

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