Vertebrate Genome Biology at the Broad Institute

The Broad Institute has been sequencing a large number of vertebrate genomes with the goals of annotating the human genome, understanding vertebrate genome evolution and enhancing biology in various model organisms.

The completion of the 29 Mammals Project has led to the identification 3.6 million conserved elements (~4.2%) in the human genome. Of these, 30% were clearly annotated (protein coding, regulatory elements, etc.,) another 30% showed overlap with chromatin markers, while the remaining 40% were novel functionality.

NHGRI has approved the sequencing of an additional 150-200 mammals.  This will allow us to develop a map of functional constraint in the human genome to single-base resolution.  30 genomes were chosen in Phase I, and of these, 11 have been sequenced, assembled and released, with the others soon to follow.  In addition to assembling these genomes, we have also been generating RNA-Seq data for a number of species across the mammalian tree.

We have also sequenced a number of non-mammalian vertebrates, including the African coelacanth Latimeria chalumnae.  Known as a “living fossil,” this fish sits at the key node between fish and tetrapods.  We have gathered a number of insights from this genome, including important information on vertebrate adaptation to land, fin-to-limb transition and confirmation of the dispute between coelacanth and lungfish position relative to vertebrates (the lungfish is closer.)  This project highlights the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution.