Tilapia Genome Project

The 3000 species of cichlid fish, which includes tilapia, are found in a variety of habitats in Central and South America, Africa, and India. From an evolutionary point of view, the most interesting cichlid species are the 1500 species that recently diverged in the lakes of East Africa. Remarkably, the cichlids of Lake Tanganyika have diverged into 250 species in the past 6-8 million years, and the 500 Lake Victoria species and the 700 Lake Malawi species diverged in only the past 1 million years. For the scientific community, these species provide a natural mutant screen superior to any chemical mutagenesis. The cichlids are especially diverse in tissues and systems such as the endocrine and nervous systems that are related to the neural crest, a vertebrate-specific developmental germ layer. Cichlids are also valuable model organisms for the study of sex determination evolution, speciation and behavior. The combination of a sequenced tilapia genome and the wide variety of recently evolved cichlid behaviors and morphological traits will provide a unique opportunity to study social dominance, territoriality, sexual selection, and feeding behaviors, as well as a wide variety of neural crest derived traits.

The Broad Institute has generated a high quality draft from a Nile tilapia, Oreochromis niloticus. The Nile tilapia is 10-15 million years diverged from the East African lake cichlids, and provides a good outgroup for the study of the remarkable speciation among the cichlids in those lakes. In addtion, the Broad has produced high quality drafts of 4 additional cichlid species representing a broad cross-section of the East African Lake lineages:  Astatotilapia burtoni, Malawi (Maylandia) zebra, Pundamila nyererei and Neolamprologus brichardi.  These genomic resources will not only help researchers address important questions about vertebrate evolution, but will also enable the study of behavior, immunology, and toxicology. They will also contribute to the maintenance and improvement of the tilapia as an important food source in over 100 countries and one of the primary sources of protein in the developing world. RNA-seq from a wide spectrum of tissues has been completed to aid in genome annotation for all five cichlid species.

Current Status - Oreochromis niloticus
Initial Illumina Sequence complete
Genome Assembly High-quality draft, released
Data release summary
Initial assembly OreNil 1.0, released January 2011

Current Status - Astatotilapia burtoni
Initial Illumina Sequence complete
Genome Assembly High-quality draft, released
Data release summary
Initial assembly HapBur 1.0, released October 2011

Current Status - Malawi zebra
Initial Illumina Sequence complete
Genome Assembly High-quality draft, released
Data release summary
Initial assembly MayZeb 1.0, released October 2011

Current Status - Neolamprologus brichardi
Initial Illumina Sequence complete
Genome Assembly High-quality draft, released
Data release summary
Initial assembly NeoBri 1.0, released May 2011

Current Status - Pundamila nyererei
Initial Illumina Sequence complete
Genome Assembly High-quality draft, released
Data release summary
Initial assembly PunNye1.0, released October 2011

For more information on this project, please contact us at vertebrategenomes@broadinstitute.org.

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