Metabarcoding and NGS Laboratory
Characterizing meiofauna and planktonic communities of the marine ecosystems always been a hard and time-consuming process due to the size of the individuals, the high diversity of the groups and scarcity of taxonomic specialists. The use of DNA barcoding coupled with Next Generation Sequencing techniques represent a leap forward in our ability for biodiversity estimation of those organisms. These groups of organisms are becoming more and more relevant for monitoring the heath of the ecosystems and evaluating the impacts of human activities.
We aim at developing and testing rapid biodiversity assessment methods that will help to understand ecosystem change while at the same time reducing processing time and costs. We apply community DNA metabarcoding and eDNA methods in our NGS –Lab which is equipped with an Illumina MiSeq sequencer. In the field of metabarcoding, our work is being conducted on optimizing the procedure of DNA extraction, PCR and the development of bioinformatics pipelines to trim, filter and analyze the illumina reads and assign taxonomic identifications to the putative OTUs or Sequence Variants. In this regard, our research is primarily focused on the two frequently used gene fragments mtDNA COI barcode and the V1 & V2 hypervariable region of 18S rRNA to estimate the diversity and examine the accuracy of the pipeline as well as the ability of those markers to evaluate the fauna. In order to obtain better identification of the sequences we, produce our own reference libraries by barcoding taxonomically identified specimens using Sanger sequencing. The accurate taxonomic work is crucial at this step for which we work closely together with specialist. We use these libraries in combination to open access NCBI repositories.
The metabarcoding laboratory also performs analyses of microbiomes associated with target macro and megafauna organisms like deeps-sea sponges and crustaceans.
We also use restriction associated DNA-markers (in our lab we use 2bRADs) to assess the genetic connectivity between populations of marine species for different projects.