Vertebrate genome sequencing using nanopore technology

3 Augustus 2017, During the past two decades, genomics research has provided many areas of biology with vast amounts of valuable data and knowledge. With ever improving technologies for reading DNA, and rapidly reducing costs, genomics is now finding applications beyond the biology of humans and model organisms. The latest DNA sequencing technology comes in a handheld device – the MinION, developed by Oxford Nanopore Technologies.


In an article published today in Scientific Reports, an international team from the Netherlands, France, Norway and Austria (including Hans Jansen, Susanne Jong-Raadsen, and Ron Dirks from Future Genomics Technologies) demonstrates how MinION sequencing can be used to efficiently generate the genome sequence of an endangered animal, the European eel.


European eels reproduce exclusively in the Sargasso Sea, more than 6000 kilometers from mainland Europe. Therefore, all eel production and consumption currently relies on declining wild stocks. Genomic resources can form the basis for unraveling the physiological control of the eel’s reproductive cycle, as well as understanding its ecology and evolution.


The European eel genome is the first vertebrate genome to be based on nanopore sequencing. In combination with the bioinformatics methods developed in the article, this technology is promising for many other non-model organisms, as it requires only a modest investment in both sequencing equipment and computing power.


In Leiden, the tulip is the next iconic genome on the list. Like eels, tulips suffer from breeding difficulties that could be addressed using genomics technology. Until now, sequencing its genome was simply not possible, as it is more than ten times as large as the human genome. However, based on the technologies pioneered for the eel genome, Leiden-based genomics company Future Genomics Technologies is currently working on a draft genome of the tulip in collaboration with the Generade consortium.

Reference to the paper

Rapid de novo assembly of the European eel genome from nanopore sequencing reads. Scientific Reports (2017) is freely available here.

Participating organisations

Throughout Europe many institutes contributed to this study. They are the Institute of Biology of Leiden University, University of Applied Sciences Leiden, Generade Centre of Expertise in Genomics, Wageningen University & Research, and DUPAN Foundation for sustainable eel farming and fishing from the Netherlands. The Muséum National d’Histoire Naturelle of the Sorbonne Universités in France. The Norges miljø- og biovitenskapelige universitet from Norway, and from Austria the Institute of Zoology and Center for Molecular Biosciences of the University of Innsbruck.

Funding and support

This project was funded by grants from the DUPAN Foundation for sustainable eel farming and fishing, the Dutch Ministry of Economic Affairs (KB-21-001-001), the Austrian Science Foundation (FWF P26363-B25), the EU Innovative Training Network IMPRESS, and by local funds from CNRS and Generade, the Leiden Centre of Expertise in Genomics. Some of the reagents were supplied by Oxford Nanopore Technologies Ltd.

More background information can be found in the following links

Pocket-size sequencers start to pay off big. Science (2017)

Christiaan Henkel on eel and tulip genome sequencing

Oxford Nanopore Technologies

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