SINGEK: New introductory VIDEO

A new introductory video about our SINGEK Innovative Training Network is out:

We are really grateful to SINGEK fellows (including some Early Stage Researchers) who contributed to informally present our ambitions and drive!

Enjoy it!

EMBO Workshop on Comparative genomics of eukaryotic microbes

Comparative genomics of eukaryotic microbes: Dissecting sources of evolutionary diversity

EMBO Workshop, 14th-19th October, Sant Feliu (Girona)

EMBO – excellence in life sciences organizes a workshop in St Feliu de Guíxols (Girona, Spain) from 14th to 19th October 2017, which will be focused on comparative genomics of eukaryotic microorganisms.

Unicellular eukaryotes comprise the overwhelming majority of eukaryotic cellular and genomic diversity, pervading all branches of the eukaryotic tree of life. Recent sequencing efforts have significantly increased the number of unicellular eukaryotes for which genomic/cellular/proteomic data are available. Metagenomics, transcriptomics,single-cell genomics, and other approaches are being applied to unravel the ecology, physiology, diversity and evolution of microbial eukaryotes and are shedding light on fundamental questions such as the origin of the eukaryotic cell, endosymbiosis, the origin of multicellularity and the evolution of major cellular systems in eukaryotes.

Although there are conferences devoted to genomics of prokaryotes and that of plants and animals, this EMBO Workshop will be the only forum bringing together this diverse community with a range of expertise and which concentrates on microbial eukaryotes.


There is a need, particularly in organisms without large communities, to have a forum where approaches, new methodologies and datasets can be shared to the advancement of this field. In particular, three of the SINGEK project supervisors will be involved in this  EMBO conference: Thomas Richards (as organizer, University of Exeter, supervisor of ESR11), Ramiro Logares (as speaker. CSIC Institut De Ciències Del Mar, supervisor of ESR2) and Iñaki Ruiz-Trillo (also as speaker, IBE: Institute of Evolutionary Biology CSIC – UPF, supervisor of ESR3).


You can follow updates from this EMBO Workshop in its Website or via Facebook.

Abstract Submission is open until 15th August!!


SINGEK: Iñaki Ruiz-Trillo elected as new EMBO member

Iñaki Ruiz-Trillo, supervisor of “ESR3 – Uncultured opisthokonts and the origin of metazoan multicellularity“, has been elected as new EMBO – excellence in life sciences member as recognition of research excellence. He is one of the 65 outstanding life scientists in the list published by this institution this week. Congratulations Iñaki!!


Iñaki is an ICREA research professor at IBE: Institute of Evolutionary Biology (CSIC – UPF) and is currently the Principal Investigator of the Multicell Genome Lab. His group focuses on how animal multicellularity emerged from our common unicellular ancestor.


Check more details about Iñaki’s profile and his role in SINGEK here.

SINGEK: ESR3 attends to the 2017 MCAA Conference

2017 MCAA Conference and General Assembly

Our SINGEK ESR3 Konstantina Mitsi has participated in the 2017 MARIE CURIE ALUMNI ASSOCIATION (MCAA) Conference and General Assembly, which was held on Friday 24th and Saturday 25th March 2017 in Salamanca, Spain.

The program covered the main areas of interests of the MCAA members in terms of career, networking and societal challenges. The event included a poster session and a ‘science lab’ event at which delegates stepped up to the challenge of presenting their project in three minutes maximum.

More info about this event is available here.

SINGEK: ESRs participate in the ITN Science Slam Barcelona

ITN BCN Science Slam 2017

3rd of March, 21:00h, Bar mau mau (Barcelona)

Some SINGEK ESRs will participate in the ITN BCN Science Slam together with other PhD students from 6 different European Training Networks.

The ITN BCN Science Slam is a science communication event organized by the ITN Opathy (Centre for Genomic Regulation, Barcelona) where young scientists will explain their research projects in short 5/10-minute-talks that are easy to follow and afterwards the audience will get to vote.

During the short talks, the important thing will not be primarily the scientific outcome of their work, but to explain it in an understandable, entertaining and concise way. In this edition, the winner of the ITN BCN Science Slam will be invited to present his/her talk in the Science Slam of the Marie Curie Alumni Association in Salamanca, Spain on 24th of March.

The ITN BCN Science Slam will take place from 21:00 to 22:30 in the bar “mau mau”.


bar mau mau

Fontrodona 35

08004 Barcelona


You can follow news from this event via Twitter at @SINGEK_ITN., @OpathyITN


SINGEK: New paper about SCG of oceanic unculturable picoeukaryotes

We are glad to announce that a new SINGEK paper is out in Scientific Reports/ NatureJournal:

“Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells”

J-F. Mangot, R. Logares, P. Sánchez, F. Latorre, Y. Seeleuthner, S. Mondy, M. E. Sieracki, O. Jaillon, P. Wincker, C. de Vargas and R. Massana

Comparison of tetranucleotide frequencies of SAGs in an ESOM map.

Pico-sized eukaryotes play key roles in the functioning of marine ecosystems, but we still have a limited knowledge on their ecology and evolution. The MAST-4 lineage is of particular interest, since it is widespread in surface oceans, presents ecotypic differentiation and has defied culturing efforts so far. Single cell genomics (SCG) are promising tools to retrieve genomic information from these uncultured organisms. However, SCG are based on whole genome amplification, which normally introduces amplification biases that limit the amount of genomic data retrieved from a single cell. Here, we increase the recovery of genomic information from two MAST-4 lineages by co-assembling short reads from multiple Single Amplified Genomes (SAGs) belonging to evolutionary closely related cells. We found that complementary genomic information is retrieved from different SAGs, generating coassembly that features >74% of genome recovery, against about 20% when assembled individually. Even though this approach is not aimed at generating high-quality draft genomes, it allows accessing to the genomic information of microbes that would otherwise remain unreachable. Since most of the picoeukaryotes still remain uncultured, our work serves as a proof-of-concept that can be applied to other taxa in order to extract genomic data and address new ecological and evolutionary questions.

SINGEK: ESRs participate in the 2017 WORKSHOP on GENOMICS

Workshop on Genomics 2017

8th-21th January, Český Krumlov (Czech Republic)


All SINGEK ESRs will start the New Year by attending to this workshop as their first scientific training activity. This workshop has in the organizing committee Karin Rengefors (Lund University), supervisor of “ESR 13 – Next-Generation microbial population genetics using single-cell genomics”.

You can follow news from this workshop in its website or via Twitter at @evomics.

SINGEK: Opening Meeting including all 15 recruited ESRs

More than 30 researchers, including the 15 recruited Early Stage Researchers (ESRs), have met for the SINGEK Opening Meeting at the Institute of Marine Sciences, Barcelona (7-9 November, 2016).

SINGEK project (Promoting SINgle cell GEnomics to explore the ecology and evolution of hidden microeuKaryotes) will  focus on the study of microeukaryotes in natural systems, among which we can find protozoa, algae and microscopic fungi. The study of microeukaryotes is essential to comprehend eukaryotic diversity and evolution, including the origin of plants and animals, and also to better understand their role  in all ecosystems. In order to address this challenging task, however, the use of new and more accurate molecular techniques is required.

“The SINGEK project has a double objective. On the one hand, study the genomes of novel and uncultured microeukaryotes with the novel Single Cell Genomics (SCG) tool, applied until now in other fields as cancer research. And on the other hand, provide a unique and structured PhD training programme to train a new generation of scientists with the highest expertise in SCG, including also transferable skills essential for successful career development” explains Ramon Massana, ICM researcher in the Marine Biology and Oceanography department, and SINGEK Coordinator.

SINGEK will train 15 ESR from 9 different countries such as EEUU, Germany, Iran, Spain, Greece or Brazil, that will develop their research in fields related to bioinformatics, genomics, ecology and microbial evolution, under the supervision of 15 expert researchers from 12 science institutions from 5 different countries (Spain, France, Belgium, Sweden and UK). The project also counts with 8 Partner Organisations that will be involved in several tasks, as hosting students during their secondments, providing complementary training in complementary skills as scientific writing, or developing the project’s communication and outreach plan at different levels.

“All the research individual projects will cover the world of microorganisms from different perspectives, such as organisms’ interactions, marine microbial community composition and their involvement in climate change mitigation, development and improvement of SCG techniques and DNA sequencing, and other issues like multicellular organism emergence and a more complex view of the tree of life” states Iñaki Ruiz-Trillo, ICREA researcher from the Institute of Evolutionary Biology (CSIC-UPF) and also member of the SINGEK Coordinating Team.

SINGEK has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie program. The project has a duration of 4 years and a budget of 3,9M€.

Tara Oceans PhD offer / SYMBIOME

PhD POSITION AVAILABLE at Station Biologique de Roscoff – CNRS / UPMC

The project “SYMBIOME: an eco ‐systemic approach to eukaryotic symbioses in global photic plankton” offers a PhD position to a highly-motivated student with taste for ecology and biostatistics (and no fear for bioinformatics and plankton) to “unravel the main eukaryotic (protist) holobionts in the world plankton using the power of Tara Oceans size-fractionated combined datasets (metaB, T, G, microscopy)”.

This PhD thesis will be co-­supervised by Colomban de Vargas and Stéphane Audic (bioinformatics and statistics) at CNRS-­Roscoff, and Eric Pelletier (bio/systems ‐ informatics) at Genoscope.

– basic training in biology and ecology.
– skills in biostatistics (programming language Perl or Python, and R, in Unix/Linux)
– interest in ecology and evolution of marine eukaryotes and symbioses
– techniques of molecular biology and ecology

Send an email to Colomban de Vargas (vargas@sb-­ and Eric Pelletier ( including:
– your detailed CV, including your academic record and research experience
– a motivation statement (why you are interested in this project, max. 500 words)
– a short essay commenting a paper you have recently read and that changed your vision of science (max.300 words).

2nd edition of the EukRef Workshop in Barcelona

2nd edition of the EukRef Workshop

28th November – 2nd December 2016, Barcelona

This second workshop that will take place at the Institute of Marine Sciences in Barcelona from November 28th to December 2nd, 2016. It will bring together taxonomists with expertise in individual lineages that span the eukaryotic tree of life to curate reference 18S rDNA sequences of these lineages by incorporating knowledge of phylogenetic, morphological, and/or environmental contextual data. This second edition will be particularly (but not exclusively) focused on Amoebozoa and Rhizaria. During the workshop, the working group will integrate the curation efforts on individual eukaryotic groups into a biological data warehouse consisting of curated sequences, flexible taxonomy, and phylogenetic trees and their underlying sequence alignments. We will further use this 18S rDNA reference database to investigate the environmental distribution of eukaryotic microbes from large-scale HTES datasets. Each curator is encouraged to use their curated data to address research questions of interest. It will be discussed how to tackle such projects and encourage participants to publish their results.

Thanks to the generous contribution of the Moore Foundation, the cost of housing, breakfast and lunch, and reimburse for the cost of flights up to $400 will be covered for participants within Europe and $1500 for those from the rest of the world.

Application deadline: September 16th 2016

Follow EUKREF updates in Twitter: @EukRef