0 avis
Towards an universal genome-based DNA barcode-The PhyloAlps project
Archive ouverte
Edité par CCSD -
International audience. The DNA barcoding initiative, proposed in 2003, represented a big step forward in standardized DNA-based species identification. It corresponds to the use of a single or few small portions of the genome (= standard barcodes) as a discrete taxonomic character for identifying unknown specimens by comparison with a reference database. The barcoding initiative was very successful and led to the collaboration of many teams around the world, producing extensive reference databases. However, the standard barcodes were designed in the context of Sanger sequencing, and the recent development of next-generation sequencing (NGS) allows further developments of the barcoding initiative. In light of the PhyloAlps project aiming to sequence the whole alpine flora, we suggest to complement the standard barcode strategy with an approach taking advantage of the power of NGS. We propose to develop an extended barcode, simply composed of one or two gigabases of sequence reads obtained using shotgun sequencing of genomic DNA. From this extended barcode, we demonstrate for both an animal dataset and for a plant dataset that it is possible to extract the initial standard barcodes, the whole organelle genomes, the whole nuclear ribosomal tandem repeats, and a collection of sequence reads corresponding to single-copy DNA regions. Such an extended barcode can be generated not only for multicellular eukaryotes, but also for microorganisms via single-cell sequencing. As a consequence, the extended barcode has the potential of being truly universal, encompassing organisms from the three domains of life (eukaryotes, bacteria, archaea). After a four-year sampling effort, the PhyloAlps 6000-sequence dataset will be produced by the end of 2015 at Genoscope in France. This tremendous dataset can be considered as a large pilot experiment for this new DNA barcoding strategy.
Consulter en ligne
Suggestions
Du même auteur
