Vertebrate Genome Biology at the Broad Institute

The Broad Institute has sequenced a large number of vertebrate reference genomes with the goals of annotating the human genome, understanding vertebrate genome evolution and enhancing biology in various model organisms.  These reference genomes have also provided a critical growing resource for comparative genomic analyses.

The European Rabbit Orytcolagus cuniculus is a critical species of both evolutionary and economic importance. We sequenced 24 sub-species and were able to identify signatures of selection and domestication events.  We concluded that rabbit domestication is primarily a function of large numbers of “soft sweeps” acting through the regulation of behavioral genes.

The Ferret Mustela putorius furo is an important model organism for influenza host-response research.  We have produced a differential expression analysis and transcriptome characterization on H1N1 infected vs. non-infected samples using RNA-Sequencing technology, which will greatly aid in the further study of influenza in this model organism.

The African lake cichlid system (5 species) is a fantastic system for the study of adaptive radiations. We have generated high quality transcriptomes for these species.  Comparisons of these data and the genomes assemblies provide valuable insights to the evolutionary underpinnings of adaptive radiations.

The African coelacanth Latimeria chalumnae , known as a “living fossil,” is a key node between fish and tetrapods.  From this study we have gained key information on vertebrate adaptation to land, fin-to-limb transition and confirmation of the dispute between coelacanth and lungfish position relative to vertebrates, all fundamental questions in understanding tetrapod evolution.