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Thesis Subject EMBC 2013-2014 Alexia Semeraro
Transcript of Thesis Subject EMBC 2013-2014 Alexia Semeraro
Next-generation sequencing (NGS)
Revolution : - thousands or millions of sequences
- low-cost sequencing
-Barcodes = short standardized genomic sequences
-Taxonomic identification and biodiversity studies
-Comparative biodiversity analyses
-Currently used on multicellular eukaryotes but with the ambition of studying the entire diversity of life
-Same principle that associates DNA sequences
to taxa (lineage, species, genus, family) for
estimating biodiversity of environmental samples
Based on extracting total (and often degraded) DNA from environmental samples (water, sediments) to analyze biotic assemblages
-PCR-amplifying Barcoding genes
= representative of the organisms present in the environment
- Employed for Prokaryotes
- Inventory of eukaryotic communities
Can potentially detect any kind of organism in
Sets of primers need to be
PCR amplicons obtained with adequate primers from the total DNA extracted from an environmental sample can be considered as a mirror of the biodiversity present in the environment.
Focused on biodiversity gradients created around shellfish farms in
the Cantabric coast (North Iberia).
Two estuaries, Villaviciosa and Eo:
Suffers from high pressures of human activity due to mollusc culture: clams and oysters
Biodiversity gradient associated to each type of these farms
(oysters, clams) will be determined by comparison between the profiles.
-> Comparative biodiversity analyses
Promotor / Supervisor:
Dr.Eva Garcia-Vazquez and Prof.Yaisel Juan Borrell Pichs
Environmental degradation caused by marine farms
causes drastic changes in biodiversity :
- enhancing invasions
- endangering native species
Eukaryotic metabarcoding profile will be analyzed from environmental samples taken at different distances from the shellfish farming areas.
Some sampling areas (not disturbed by aquaculture activities and near to those estuaries in the Cantabric coast ) will be used as a reference or control for comparison.
-> Using these primers for vertebrates : Uni-Minibar 130pbs and
16Smam 140pbs, COI 658pbs (Ficetola et al. 2010)
and for microalgae (expectedly diatoms) : rbcL
(Stoof-Leichsenring et al. 2012)
-> With NGS Ion Torrent amplicon sequencing methodology
Methodology for analyzing biodiversity from environmental samples based on next-generation DNA sequencers.
After collecting environmental samples in the field, extracting DNA and amplifying with universal primers that target very short DNA fragments (less than 150 base pairs), hundreds or thousands of amplified DNA molecules are sequenced using next-generation sequencers. Using a reference DNA database, the taxa these sequences come from are identified and used to estimate different biodiversity parameters.
- Workplan Thesis subject
- Valentini, A., F. Pompanon, et al. (2009). "DNA barcoding for ecologists." Trends in Ecology & Evolution 24(2): 110-117.
- Bittner, L., S. b. Halary, et al. (2010). "Some considerations for analyzing biodiversity using integrative metagenomics and gene networks." Biology direct 5(1): 47.
- Ficetola G. F. et al. (2010). "An In silico approach for the evaluation of DNA barcodes." BMC Genomics, 11:434.
- Stoof-Leichsenring K. R. et al. 2012. "Hidden diversity in diatoms of Kenyan Lake Naivasha: a genetic approach detects temporal variation." Molecular Ecology 21, 1918–1930.
- eDNA barcoding and metabarcoding - General introduction 2013 Symposium - Eva BELLEMAIN - SpyGen
Thank you for your attention !