DNA barcoding; Phylogenomics; Protists; Metagenetics; Next-gen sequencing; Environmental DNA
Pawlowski Jan, Esling Philippe, Lejzerowicz Franck, Cordier Tristan, Visco Joana, Martins Catarina, Kvalvik Arne, Staven Knut, Cedhagen Tomas (2016), Benthic monitoring of salmon farms in Norway using foraminiferal metabarcoding, in Aquaculture Environment Interactions
, 8, 371-386.
Laroche Olivier, Wood Susanna A, Tremblay Louis A, Ellis Joanne I, Lejzerowicz Franck, Pawlowski Jan, Lear Gavin, Atalah Javier, Pochon Xavier (2016), First evaluation of foraminiferal metabarcoding for monitoring environmental impact from an offshore oil drilling site., in Marine environmental research
, 120, 225-35.
Pawlowska Joanna, Zajaczkowski Marek, Lacka Magdalena, Lejzerowicz Franck, Esling Philippe, Pawlowski Jan (2016), Palaeoceanographic changes in Hornsund Fjord (Spitsbergen, Svalbard) over the last millennium: new insights from ancient DNA, in CLIMATE OF THE PAST
, 12(7), 1459-1472.
Pawlowski J, Lejzerowicz F, Apotheloz-Perret-Gentil L, Visco J, Esling P (2016), Protist metabarcoding and environmental biomonitoring: Time for change., in European journal of protistology
, 55(Pt A), 12-25.
Pochon X, Wood S A, Keeley N B, Lejzerowicz F, Esling P, Drew J, Pawlowski J (2015), Accurate assessment of the impact of salmon farming on benthic sediment enrichment using foraminiferal metabarcoding., in Marine pollution bulletin
, 100(1), 370-82.
Esling Philippe, Lejzerowicz Franck, Pawlowski Jan (2015), Accurate multiplexing and filtering for high-throughput amplicon-sequencing., in Nucleic acids research
, 43(5), 2513-24.
Visco Joana Amorim, Apothéloz-Perret-Gentil Laure, Cordonier Arielle, Esling Philippe, Pillet Loïc, Pawlowski Jan (2015), Environmental Monitoring: Inferring the Diatom Index from Next-Generation Sequencing Data., in Environmental science & technology
, 49(13), 7597-605.
Lejzerowicz Franck, Esling Philippe, Pillet Loïc, Wilding Thomas A, Black Kenneth D, Pawlowski Jan (2015), High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems., in Scientific reports
, 5, 13932-13932.
Pawlowski Jan, Esling Philippe, Lejzerowicz Franck, Cedhagen Tomas, Wilding Thomas A (2014), Environmental monitoring through protist next-generation sequencing metabarcoding: assessing the impact of fish farming on benthic foraminifera communities., in Molecular ecology resources
, 14(6), 1129-40.
Pawlowski Jan, Lejzerowicz Franck, Esling Philippe (2014), Next-generation environmental diversity surveys of foraminifera: preparing the future, in Biological Bulletin
, 227(2), 93-106.
Pawlowski J, Lejzerowicz F, Esling P (2014), Next-generation environmental diversity surveys of foraminifera: preparing the future., in The Biological bulletin
, 227(2), 93-106.
Next-gen sequencing (NGS) is in process of becoming the most important molecular tool for research in evolution and ecology. In particular, the new benchtop systems offer rapid and reasonably low-cost instruments to generate large amount of genomic data. The constant flow of ultra-deep sequence data is radically changing our view on diversity of genomes and organisms. The most striking effect of NGS-based technologies is the discovery of an extraordinary richness of prokaryotic and microeukaryotic communities.The goal of this project is to purchase the Illumina MiSeq personal sequencing system. This highly automated and easy-to-use benchtop machine will serve for acquisition of sequence data in several projects on evolution and ecology of microeukaryotes being developed by the applicants and collaborators. Most of these projects focus on the assessment and monitoring of microeukaryotic diversity in various ecosystems, ranging from deep-sea to freshwater and soil environments. The MiSeq system will be employed to obtain sequence data from hundreds of environmental DNA samples collected in the framework of SNSF and other projects. These data will be used: (1) to assess the richness of marine protists and test the preservation of their DNA in deep-sea subsurface sediments; (2) to examine the impact of biogeography and environmental factors on diversity and distribution patterns of peatlands protists; (3) to evaluate the use of protists as bioindicators in forensic research; and (4) to assess the diversity of terrestrial microbiota (NCCR submitted and ongoing pilot projects). The NGS data will also help realizing several metagenetic projects using protists in biomonitoring and biosecurity, and supported by the Federal Office for the Environment, Sciex and European Community programs.The Miseq sequencing platform will also be used to acquire the genomic and transcriptomic data for evolutionary studies of microeukaryotes. Since several years the applicants participate in the effort to reconstruct the tree of eukaryotes based on phylogenomic data. Today, the main challenge of this research is to obtain multigene sequence data for the huge diversity of mostly uncultivable protists. The access to MiSeq will boost this effort by increasing the number of examined species, for which only limited amounts of DNA/RNA are available. Until now all our projects have been realized either by Sanger sequencing or by using NGS service of different public and private institutions. The use of NGS approach, however, was limited by high costs and some technical difficulties related to particular requirements of different sequencing systems. We believe that most of these problems could be resolved by investing in our own sequencing platform. Compared to other NGS technologies, the MiSeq system has several advantages, such as relatively long reads, appropriate throughput, short run times, minimal hands-on time, cost-effectiveness and the lowest error rate reported among sequencing platforms. It is also one of the few NGS systems, which does not require a specially trained technician to operate and maintain it. Its easy workflow and its performance correspond perfectly to the scale of our research. For all these reasons, the MiSeq appears as an ideal instrument for our needs, and the best solution to enhance the realization of our projects.