Project

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High-throughput sequencing for research on evolution and ecology of microeukaryotes

Applicant Pawlowski Jan Wojciech
Number 150817
Funding scheme R'EQUIP
Research institution Département de Génétique et Evolution Faculté des Sciences Université de Genève
Institution of higher education University of Geneva - GE
Main discipline Zoology
Start/End 01.12.2013 - 30.11.2014
Approved amount 60'000.00
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All Disciplines (3)

Discipline
Zoology
Molecular Biology
Ecology

Keywords (6)

DNA barcoding; Phylogenomics; Protists; Metagenetics; Next-gen sequencing; Environmental DNA

Lay Summary (French)

Lead
Le séquençage à haut-débit a révolutionné la recherche en génomique et métagénomique, en permettant d’obtenir une grande quantité des séquences d’ADN rapidement et à un prix modéré. Il existe sur le marché plusieurs systèmes de séquençage qui diffèrent par la taille et le nombre des séquences générées. Parmi ces systèmes, la plateforme Miseq d’Illumina convient particulièrement aux travaux qui nécessitent une quantité moyenne des séquences, tels que le séquençage de l’ADN environnemental.
Lay summary

Work Programme 2014-2015 Horizon 2020 Specific Programme for Societal Challenge 2: FOOD SECURITY, SUSTAINABLE AGRICULTURE, MAR

Work Programme 2014-2015 Horizon 2020 Specific Programme for Societal Challenge 2: FOOD SECURITY, SUSTAINABLE AGRICULTURE, MAR

Lead

Le séquençage à haut-débit a révolutionné la recherche en génomique et métagénomique, en permettant d’obtenir une grande quantité des séquences d’ADN en très peu de temps et à un prix modéré. Grâce au développement des nouvelles technologies, il existe sur le marché plusieurs systèmes de séquençage qui diffèrent principalement par la taille des séquences générées, leur nombre et le temps nécessaire pour les obtenir. Parmi ces différents systèmes, la plateforme Miseq d’Illumina est le mieux adapté aux travaux qui nécessitent une quantité moyenne des séquences, tels que le séquençage de l’ADN environnemental ou des petits génomes mitochondriaux et chloroplastiques.

Contenu et objectifs du travail de recherche

L’objectif de ce projet est d’acquérir un séquenceur à haut-débit du type Illumina Miseq. Cet appareil va être utilisé principalement pour séquencer les communautés des protistes dans les échantillons environnementaux. Il permettra d’évaluer la richesse des eucaryotes microbiens, de découvrir les nouvelles lignées et d’estimer leur abondance relative. En plus il permettra d’acquérir des données génomiques et transcriptomiques des protistes non-cultivables pour lesquels une quantité très limitée du matériel génétique est disponible.

Contexte scientifique et social du projet de recherche

Les résultats des différents projets qui seront réalisés avec le nouveau séquenceur contribueront à la meilleure compréhension de l’évolution des protistes et de leur rôle dans le fonctionnement des écosystèmes. L’accès direct au séquenceur facilitera aussi le développement des diverses applications de l’étude de l’ADN environnemental, en particulier dans les domaines du monitoring environnemental et le diagnostic écologique.

 

 

Direct link to Lay Summary Last update: 22.11.2013

Responsible applicant and co-applicants

Publications

Publication
Benthic monitoring of salmon farms in Norway using foraminiferal metabarcoding
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.
First evaluation of foraminiferal metabarcoding for monitoring environmental impact from an offshore oil drilling site.
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.
Palaeoceanographic changes in Hornsund Fjord (Spitsbergen, Svalbard) over the last millennium: new insights from ancient DNA
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.
Protist metabarcoding and environmental biomonitoring: Time for change.
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.
Accurate assessment of the impact of salmon farming on benthic sediment enrichment using foraminiferal metabarcoding.
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.
Accurate multiplexing and filtering for high-throughput amplicon-sequencing.
Esling Philippe, Lejzerowicz Franck, Pawlowski Jan (2015), Accurate multiplexing and filtering for high-throughput amplicon-sequencing., in Nucleic acids research, 43(5), 2513-24.
Environmental Monitoring: Inferring the Diatom Index from Next-Generation Sequencing Data.
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.
High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems.
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.
Environmental monitoring through protist next-generation sequencing metabarcoding: assessing the impact of fish farming on benthic foraminifera communities.
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.
Next-generation environmental diversity surveys of foraminifera: preparing the future
Pawlowski Jan, Lejzerowicz Franck, Esling Philippe (2014), Next-generation environmental diversity surveys of foraminifera: preparing the future, in Biological Bulletin, 227(2), 93-106.
Next-generation environmental diversity surveys of foraminifera: preparing the future.
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.

Collaboration

Group / person Country
Types of collaboration
OFEV/BAFU - Office de l'Environment Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Industry/business/other use-inspired collaboration
Dr. A. Gooday, NOC Southampton Great Britain and Northern Ireland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Industry/business/other use-inspired collaboration
Water Ecology Service, Canton of Geneva Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Industry/business/other use-inspired collaboration
Vital-IT, University of Lausanne Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Research Infrastructure
Genomic Platform, University of Geneva Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Research Infrastructure
Dr. S. Bowser, Wadsworth Center United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Dr. T. Wilding, SAMS Oban Great Britain and Northern Ireland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Industry/business/other use-inspired collaboration
Dr. W. Majewski, Polish Academy of Sciences Poland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Nicolas Salamin, University of Lausanne Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Bat Sheva Live Forams Workshop Talk given at a conference Foraminiferal DNA metabarcoding applied to benthic monitoring: promises and challenges 11.09.2016 Eilat, Israel Pawlowski Jan Wojciech;
Environmental Genomics Workshop Talk given at a conference Beyond the limits of traditional biomonitoring: novel ecogenomic indices for biodiversity assessment 02.06.2016 St. Johns, Canada Pawlowski Jan Wojciech;
Séminaire Ecotox Individual talk Environmental DNA metabarcoding as a new tool for biomonitoring: promises and challenges 22.03.2016 Lausanne, Switzerland Pawlowski Jan Wojciech;
AE2015 Talk given at a conference Environmental DNA surveys for benthic monitoring of salmon farms 20.10.2015 Rotterdam, Netherlands Pawlowski Jan Wojciech;
European Congress of Protistology ECOP VII Talk given at a conference Protist metabarcoding and its applications 05.09.2015 Seville, Spain Pawlowski Jan Wojciech;
6th International Barcode of Life Conference Talk given at a conference Inferring biotic indices from molecular data 08.08.2015 Guelph, Canada Pawlowski Jan Wojciech;
SEFS9 Talk given at a conference Inferring biotic indices from molecular data 06.07.2015 Genève, Switzerland Pawlowski Jan Wojciech;
Séminaire Eawag Individual talk Environmental monitoring in the NGS era 09.05.2015 Eawag, Switzerland Pawlowski Jan Wojciech;
World Conference on Marine Biodiversity Talk given at a conference Next-generation environemntal metagenomics: a new tool for identification and assessment of deep-sea micro- and meiobenthic diversity 14.10.2014 Qingdao, China Pawlowski Jan Wojciech;
International Environmental Omics Synthesis Conference, EOS 2014 Talk given at a conference High-throughput molecular barcoding as a tool for assessment and monitoring the environmental impact associated with aquaculture 17.09.2014 Liverpool, Great Britain and Northern Ireland Pawlowski Jan Wojciech;


Self-organised

Title Date Place
Workshop on application of genomic tools for biomonitoring of marine environment: from technology to legal and socio-economic aspects 04.04.2016 Genève, Switzerland
Exploring and testing Eukaryotic-omics 24.04.2014 University of Geneva, Switzerland

Use-inspired outputs


Start-ups

Name Year

Associated projects

Number Title Start Funding scheme
141233 Adaptive evolution and key innovation in Neotropical fishes 01.11.2012 Project funding (Div. I-III)
179125 Molecular evolution and ecology of Foraminifera and related protists 01.05.2018 Project funding (Div. I-III)
140785 Evolutionary developmental genetics of ?phenotypic novelties and convergences 01.06.2012 Project funding (Div. I-III)
146342 The genetic basis of evolutionary constraints 01.04.2014 SNSF Professorships
159709 Molecular evolution and ecology of Foraminifera and related protists 01.04.2015 Project funding (Div. I-III)
141188 The effect of cadavers on soil ecology: biotic and functional responses (CADAVER) 01.08.2012 Project funding (Div. I-III)
140766 Molecular evolution and ecology of Foraminifera and related protists 01.04.2012 Project funding (Div. I-III)
182531 Biodiversity and biogeography of soil protists in continental and oceanic islands 01.01.2019 Project funding (Div. I-III)
143960 Is everything everywhere? A metabarcoding approach to protist biogeography 01.02.2013 Project funding (Div. I-III)

Abstract

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.
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