Tetraodon Project Information

Contents

Who are we?

The Eli and Edythe L. Broad Institute is a partnership among MIT, Harvard and affiliated hospitals and the Whitehead Institute for Biomedical Research. Its mission is to create the tools for genomic medicine and make them freely available to the world and to pioneer their application to the study and treatment of disease.

Questions about the project should be directed to annotation-webmaster@broad.mit.edu.

What is Tetraodon nigroviridis?

Tetraodon nigroviridis Tetraodon nigroviridis

Tetraodon nigroviridis is a freshwater pufferfish of the order Tetraodontiformes and lives in the rivers and estuaries of Indonesia, Malaysia and India. This species is 20-30 million years distant from Fugu rubripes, a marine pufferfish from the same family.

The gene repertoire of T. nigroviridis is very similar to that of other vertebrates. However, its relatively small genome of 385 Mb is eight times more compact than that of human, mostly because intergenic and intronic sequences are reduced in size compared to other vertebrate genomes.

These genome characteristics along with the large evolutionary distance between bony fish and mammals make Tetraodon a compact vertebrate reference genome - a powerful tool for comparative genetics and for quick and reliable identification of human genes.

Sequencing Tetraodon

We have been funded by the National Human Genome Research Institute (NHGRI) to produce shotgun sequence of the Tetraodon nigriviridis genome. Our strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated. Whole genome shotgun libraries were prepared from Tetraodon genomic DNA obtained from the laboratory of Jean Weissenbach at Genoscope. A plasmid library with an average insert size of 4 kb was prepared from randomly sheared and sized-selected DNA. Both ends of each plasmid were sequenced.

Additional sequence data of approximately 2.5X coverage of Tetraodon has also been generated by Genoscope in plasmid and BAC end reads. Broad and Genoscope intend to pool their data and generate whole genome assemblies.

Data releases

In advance of a completed assembly of the Tetraodon data, we are making sequence and quality files for the individual reads available for download.

Data Version 10/31/01: Currently reads representing an estimated 2.5X coverage of the Tetraodon genome are available.