# The PhyloAlps Project

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### About
Biodiversity is now commonly described by DNA based approches. Several actors are currently using DNA to describe biodiversity, and most of the time they use different genetic markers that is hampering an easy sharing of the accumulated knowledges. Taxonomists rely a lot on the DNA Barcoding initiative, phylogeneticists often prefer markers with better phylogenic properties, and ecologists, with the coming of the DNA metabarcoding, look for a third class of markers easiest to amplify from environmental DNA. Nevertheless they have all the same need of the knowledge accumulated by the others. But having different markers means that the sequences have been got from different individuals in different lab, following various protocols. On that base, building a clean reference database, merging for each species all the available markers becomes a challenge. With the PhyloAlps project we implement **genome skimming** at a large scale and propose it as a new way to set up such universal **reference database usable by taxonomists, phylogeneticists, and ecologists**. The PhyloAlps project is producing for each species of the Alpine flora at least a genome skim composed of six millions of 100bp sequence reads. From such data it is simple to extract all chloroplastic, mitochondrial and nuclear rDNA markers commonely used. Moreover, most of the time we can get access to the complete chloroplast genome sequence and to a shallow sequencing of many nuclear genes. This methods have already been successfully applied to algeae, insects and others animals. With the new single cell sequencing methods it will be applicable to most of the unicellular organisms. The good question is now: Can we consider the genome skimming as the next-generation DNA barcode ?

*Biodiversity -
DNA Barcoding -
Taxonomy -
Next Generation Sequencing -
Organelle Genomes - Metagenomics*

### Members
* Eric Coissac
* Frédéric Boyer
* Roland Douzet
* Anthony Hombiat
* Sébastien Lavergne
* Christophe Perrier
* Cristina Roquet
* Pierre Taberlet
* Wilfried Thuiller

### Resources
* **Web site**:   
  * Homepage : [phyloalps.org]
  * Database graphic interface : [data.phyloalps.org]
  * Database SPARQL query interface : [taxo.phyloalps.org]
  * Genomic data sshfs access : [seq.phyloalps.org]
* **Article**:  
Coissac, E., Hollingsworth, P. M., Lavergne, S., & Taberlet, P. (2016). [*From barcodes to genomes: extending the concept of DNA barcoding. Molecular Ecology*](https://doi.org/10.1111/mec.13549), 25(7), 1423–1428.
* **Video**:  
[*Sequencing 6000 chloroplast genomes: the PhyloAlps project*][video] by Eric Coissac in Summer School 2016 in Metagenomics
[phyloalps.org]:http://phyloalps.org
[data.phyloalps.org]:http://data.phyloalps.org
[taxo.phyloalps.org]:http://taxo.phyloalps.org
[seq.phyloalps.org]:http://seq.phyloalps.org
[video]:http://www.france-bioinformatique.fr/sites/default/files/videos/scorms/metagenomics16/session_3/Sequencing_6000_chloroplast_genomes_the_PhyloAlps_project/scormcontent/
[article]:https://www.researchgate.net/profile/Inger_Alsos/publication/292630086_Towards_an_universal_genome-based_DNA_barcode-The_PhyloAlps_project/links/56b4762208ae1f8aa4552164.pdf