Round Goby Genome Project

Since 1990, the benthic fish species round goby (Neogobius melanostomus) has been recorded in at least 20 countries outside its native range. Major waterbodies that have been colonized include the Danube river, the Rhine river, the Baltic Sea coast, and the Great Lakes.

In the last 20 years, the round goby has increasingly attracted the attention of researchers. It has become a novel model species in the fields of detoxification research, alternative reproductive strategies, salinity tolerance, invasion biology, population genetics, and food web ecology. Also, its tremendous success has fascinating evolutionary implications. Five close relatives with similar ecology and from the same native area are also invasive, but do not even come close to the round goby colonization abilities.

To date, this novel model organism was a molecular black box. There were no cell lines, no genetic map, no RNA sequence data, and no SNP data available. We have therefore sequenced and assembled the genome of the round goby using 50x coverage PacBio sequencing, and are currently annotating gene families and pathways related to invasion, colonization, and adaptation.

What are the specifications of the round goby genome?

Size~ 1GB
TechnologyPacbio, 50x coverage
Sampleliver from a single male caught in Basel, Switzerland
Specs1364 scaffolds
N50 = 2.817.412 nt
N90 = 269.424 nt
maximum contig 19.396.355 nt
smallest contig 21.178 nt
ChromosomesNot resolved to date (08.07.2016)

Who did what?

Funding SequencingFreiwillige Akademische Gesellschaft Basel
Funding AssemblyCollaboration with Gene Myers, MPI Dresden
Read generationSylke Winkler, Dresden Genome Center
AssemblyMartin Pippel, Heidelberg Institute of Technology
Blast server and Genome browser, automated annotationTomas Larsson, University of Gothenburg

What other omics data is available?

RNA seqEmbryonic transcriptome (1-32 cell stages) from 16 clutches
DNA methylomeBrain DNA methylation data from 15 males

What is the time schedule?

We are gathering experts on individual pathways for annotation. We aim for submission of a genome publication in 2017.

Are similar projects ongoing?

The sand goby genome is one of the IMAGO species sequenced at the University of Gothenburg. We will use the two species to investigate patterns of genome evolution.

I want to know more! Can I get involved?

Send a mail to irene.adrian-kalchhauser@unibas.ch