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H2020Doctoral network2016–2020

SINGEK · Promoting SINgle cell GEnomics to explore the ecology and evolution of hidden microeuKaryotes

Horizon 2020 — Marie Skłodowska-Curie Actions

Duration
2016-01-01 → 2020-05-31
EU contribution
€3,889,393
Participants
16
Scheme
MSCA-ITN-ETN

Lines connect the coordinator with its partners. CORDIS does not always give exact coordinates for projects before 2014. These points are placed at city or country level.

Results in brief

Promoting SINgle cell GEnomics to explore the ecology and evolution of hidden microeuKaryotes

Most of the extant diversity of eukaryotes remains poorly characterized, limiting society's understanding of, for example, the rise and diversification of parasite lineages, the evolutionary origin and variability of metabolic and cellular networks, and which microbes provide certain key functions in the global environment. Classical methodologies have provided up to now limited progress in our understanding of eukaryotic biology. The SINGEK project exploited the Single cell genomics (SCG), one of the most promising modern techniques given its capacity to provide genomic information of one cell at a time, a possibility unimaginable a few years ago. Applying SCG to microbial eukaryotes was particularly challenging when compared to SCG on prokaryotes, because of target genomes of greater complexity. The exploitation of SCG in this field was crucial for two main reasons: 1) to get de novo genomes of microbial species for which a pure culture was not available, and 2) to study the cell variability of genomic data and expressed genes within a microbial population. Despite the challenges and practical barriers to explore SCG to its full potential, the main objective of the SINGEK project was to train a new generation of researchers in SCG of microbial eukaryotes and do so by addressing a set of fundamental and inter-related scientific questions on evolution and ecology. Results and data generated during this project served to consolidate the SCG approach from back to end, improving the routines for single cell sorting, for whole genome amplification and sequencing, and for bioinformatic processing (including assembly, gene prediction and functional annotation). Multiple de novo genomes, representing hidden taxa in different positions of the eukaryotic tree of life, were obtained. These new genomes were used to improve the reconstruction of the eukaryotic radiation, to unveil parasitic or symbiotic interactions, to investigate the ecological potential of unknown species in base of the gene set detected, and to study the biogeography and gene expression of uncultured lineages across natural systems. Tools to study cell to cell variation in gene content and gene expression were also developed. The new datasets and tools generated are available in both public repositories and in-house web-searching platforms prepared by SINGEK members.

Data: CORDIS, © European Union

Project objective

Environmental microbial surveys have revealed a remarkable diversity of microeukaryotic life in most ecosystems, the majority of which had previously escaped detection. From an ecological point of view this work highlighted our ignorance of critical microbial players in natural environmental processes, including primary production, biogeochemical cycling and trophic interactions such as parasitism and grazing. Consequently, our understanding of community function is partial, limiting our ability to study environmental change. While, from an evolutionary perspective, we are missing major components of the Tree of Life giving rise to a fragmented understanding of how major cellular functions have evolved. Single cell genomics (SCG), including single cell transcriptomics, is an emerging technology that has the potential to retrieve genomic information from individual uncultured microbes recovered directly from natural environments and promises to provide new tools to investigate microeukaryotes in unparalleled detail. The aim of this ITN is therefore to train a new generation of scientists with the highest expertise, in SCG, from the initial stages of cell sorting to genome sequencing and gene annotation, to the full exploitation of the data obtained. Such progress will allow the European research community for the first time to address critical ecological and evolutionary questions. SINGEK will drive training through research by both local and network-wide activities, secondments, and workshops, and by establishing an environment that extends far beyond each partner team. This training environment will also provide the transferable skills essential for successful career development. This network of well connected and highly qualified scientists with expertise in eukaryotic SCG will be ready to implement this technology beyond ecology and evolution to other fields such as biomedicine or biotechnology driving innovation across the EU.

Original text from CORDIS.

Participants

  • AGENCIA ESTATAL CONSEJO SUPERIOR DE INVESTIGACIONES CIENTIFICAS · MadridCoordinatorSpain
  • ASCIDEA COMPUTATIONAL BIOLOGY SOLUTIONS SL · BARCELONACity levelSpain
  • CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS · ParisFrance
  • COMMISSARIAT A L ENERGIE ATOMIQUE ET AUX ENERGIES ALTERNATIVES · ParisFrance
  • FLUIGENT SA · Le Kremlin-BicetreFrance
  • FUNDACIO CENTRE DE REGULACIO GENOMICA · BarcelonaSpain
  • GREENSEA SAS · Saint BeauzireFrance
  • LUNDS UNIVERSITET · LundSweden
  • MUSEUM NATIONAL D'HISTOIRE NATURELLE · ParisFrance
  • PLANCTON, DIVULGACIO I SERVEIS MARINS, SOCIEDAD CIVIL PRIVADA · AMETLLA DE MARSpain
  • THE SECRETARY OF STATE FOR ENVIRONMENT, FOOD AND RURAL AFFAIRS · LONDONUnited Kingdom
  • THE UNIVERSITY OF EXETER · ExeterUnited Kingdom
  • THE UNIVERSITY OF LIVERPOOL · LIVERPOOLUnited Kingdom
  • UPPSALA UNIVERSITET · UppsalaSweden
  • VIB VZW · ZWIJNAARDE - GENTBelgium
  • WriteScience · Grimma OT DöbenGermany

Links

Data: CORDIS, © European Union