"Sample collection for metabarcoding" Deliverables

vendredi 5 juin 2015
par  Aurélien DE JODE, Dorian GUILLEMAIN, Romain DAVID
popularité : 11%

Index of "Sample collection for metabarcoding"
1. Principle
2. Method
3. Sampling
4. Deliverables
5. To summarize
Back to protocols Index
How to cite this content :

David R., Arvanitidis C., Çinar M.E., Dubar J., Dubois S., Erga Z., Guillemain D., Sartoretto S., Thierry de Ville d’Avray L., Zuberer F., Chenuil A., Féral J.-P., (2014), with contributors : Açik Çinar S., Andral B., Aurelle D., Aysel V., Bakir K., Bellan G., Bellan-Santini D., Bouchoucha M., Celik C., Chatzigeorgiou G., Chatzinikolaou E., Chenesseau S., Dağli E., Dailianis T., Dimitriadis C., D’Iribarne C., Doğan A., Dounas C., Egea E., Elguerrabi W., Emery E., Evcen A., Faulwetter S., Gatti G., Gerovasileiou V., Güçver S.M., Issaris Y., Katağan T., Keklikoglou K., Kirkim F., Koçak F., Koutsoubas D., Marschal C., Önen M., Önen S., Öztürk B., Panayiotidis P., Pavloudi C., Pergent G., Pergent-Martini C., Poursanidis D., Ravel C., Reizopoulou S., Rocher C., Ruiton S., Sakher S., Salomidi M., Sarropoulou E., Selva M., Sini M., Sourbes L., Simboura N., Taşkin E., Vacelet J., Valavanis V., Vasileiadou A., Verlaque M. Protocols for monitoring of coralligenous habitats of mediterannean (Coralligenous based Indicators to Evaluate and Monitor the "good ecological status" of the MEDiterranean coastal waters) Protocoles de suivi du coralligène en méditerranée (Coralligenous
based Indicators to Evaluate and Monitor the "good ecological status" of the MEDiterranean coastal waters).

a. Expected results
[§ 1] 32 samples will be scraped per site? (2 profiles x 2 orientations x 2 depths x 4 replicates) (assuming a single season will be sampled). At least 3 sites will be studied, i.e. 96 samples.

b. Envisaged analyses of data
[§ 2] In NGS (Next-Generation Sequencing) platforms it is possible to label -380- samples with distinct tags, thus we will be able to analyze in a single run 126 to 380 scrapings (depending on the number of size fractions separately analysed per scraping, 1 to 3). For each one hundreds of thousands of DNA sequences will be obtained, which will be linked to species identity using existing databases or sequences from reference species obtained by ourselves. For some taxa, more than one molecular marker could be used (in 95% of the cases the COI mitochondrial gene will be used).

[§ 3] Metabarcoding analyses may allow detecting (the list is not exhaustive) :
 Fishes : the detection of eggs or juveniles of a species would reveal the role of coralligenous habitat? ? as nursery (contributing to protection, eventually feeding).
 The resident vagile macrofauna with reduced mobility : echinoderms, bivalves (excluding lithophagous ones), nudibranchs, gastropods, crustaceans.
 Opportunistic or transient macrofauna : we may find species absent in the coralligenous when adults, but which have a young stage in this habitat. 
 Bioncontructors : corallinales (Lithophyllumspp., Mesophyllum spp., some Peyssonnelliaceae), bryozoans, madreporans, tube worms (Protula sp, Serpulasp.).
 Other perennial species : green algae (e.g. Codium spp., Flabellia petiolata, Halimeda tuna, Palmophyllum crassum, etc.), brown algae (e.g. Cystoseira zosteroides, Zanardinia typus), worms (e.g. Bonelllia viridis, Bispiravolutacornis, Sabella spallanzanii, etc.), boring sponges (e.g. Cliona spp.), sponges (e.g. Acanthellaacuta, Axinella spp., Spirastrella cunctatrix, etc.), ascidians (e.g. Aplidium spp., Clavelinaspp., Halocynthia papillosa, etc.), cnidarians (e.g. Parazoanthusaxinellae, Savalia savalia, etc.,).


- Deadline : 14th December 2015
- Please add comments for each paragraph (§) by means of a corrected new version (one form per §)
- It is recommended to add scientific references if necessary

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