The Euro-Fish Project at the CSBD

The Euro-Fish initiative aims to create a genomic survey of all species of freshwater fishes of Europe in order to understand and avert the loss of biodiversity. Currently, there are believed to be about 600 native species of freshwater fishes in Europe.

The European sub-continent is rich in its diversity of natural habitats. But, due to the long period of human settlement and the high density of human populations, the European landscapes have been altered significantly by water pollution due to eutrophication from fertilizers, agriculture, urbanization of large areas, and by dams. Fishes, that are crucial for almost all food chains in all freshwater ecosystems, are more affected and threatened by human activity than other groups of organisms such as mammals and birds. 88% of EU fish stocks are overexploited and severely depleted. For 76% of all European freshwater fish it is not even known what their population dynamics are.

In order to better understand and protect Europe’s biodiversity, Euro-Fish plans to assay the genomic resources contained in the native fishes of Europe. This will help not only with better management of fish stocks, but also more generally in the implementation of better protection plans for ecosystems. This is of particular interest since freshwater fish, due to their tight interdependence to their surroundings, are a particularly suitable group in which one can study how climate change affected their distributions and adaptations to changing environmental conditions.

The CSBD and the MPI-CBG are contributing to the EURO-Fish initiative together with the University of Konstanz, Germany, the Leibniz Institute of Freshwater Ecology & Inland Fisheries Berlin, and the Zoological Research Museum Alexander Koenig, Berlin.

The Max Planck Society is funding this ambitious genome sequencing project.

Euro-Fish at the CSBD and the MPI-CBG

We have been funded to begin to sequence all of the almost 600 species of fish swimming in European fresh waters. In the initial phase, we are planning to sequence about 50 species from a given geographic area to understand how the environment shapes the evolution of genomes.

Process / Technology

Species to be sequenced are selected between collaborators and tissues are submitted to the CSBD, the MPI-CBG, and the Dresden-concept Genome Center (DCGC).

A variety of de-novo sequencing technologies are currently applied and data are combined for genome assemblies to achieve our goal of error-free, near-gapless, chromosome-level, phased and annotated assemblies.

The current genome sequencing regime involves:

  1. 60x genome coverage of PacBio SMRT (single molecule real time DNA sequencing) reads,
  2. 50x genome coverage of 10X Genomics-linked reads for intermediate-range scaffolding,
  3. one DLS map making use of Bionano optical mapping to correct potential scaffolding errors,
  4. 50x HiC-linked reads for large-scale scaffolding,
  5. HiC and 10x Genomics linked short Illumina reads will be used for error correction of individual bases in the pipeline,
  6. RNAseq data and / or PacBio IsoSeq data for genome annotation.

PacBio SMRT DNA sequencing and 10x Genomics read cloud generation are done at the DCGC. 
Bionano optical mapping will be established in Q4/2018 at the DCGC. 
For HiC is done exclusively with a commercial supplier (Arima Genomics, Inc. US). 

The Genome assembly pipeline and Dazzler:

The Dresden genome assembling pipeline consists of two activities:

a) We are setting up a pipeline to generate error-free, near-gapless, chromosome-level and phased and assemblies making use of existing algorithms and software tools such as FALCON unzip, MARVEL, Scaff10X, TGH, Salsa, and, PBJelly.

b) We are working on concepts and algorithms to analyze, understand and error correct long PacBio sequencing reads (The Dresden AZZembLER for long read DNA projects: dazzler).  These pipelines will lead to a significant improvement of the assembly process in terms of accuracy, assembly continuity and finally required computing time.

Data use policy

A data use policy is currently being drafted by the Euro-Fish project team. In the meantime, for all related species get in touch with Sylke Winkler.