Tag: Ingo Braasch

Genomic News From an Old Fish: Understanding Gene Regulation by Sequencing the Genome of a Living Fossil, the Spotted Gar (Lepisosteus oculatus)

Presenter: Margo Werner, Biology

Poster: D-3

Mentor: Ingo Braasch, John Postlethwait Biology

Cis-regulatory elements (CREs) are important regions of the genome that modulate the expression of nearby genes. However, their role in the evolution of genes is not yet well understood. To examine the function and evolution of CREs in fish, we study the spotted gar (Lepisosteus oculatus). The gar is a ‘living fossil’ that diverged from teleost fishes just before a teleost-specific whole genome duplication. Comparing the genome sequence of gar to teleosts allows us to investigate the appearance of CREs in relation to this genome duplication. We screen a genomic library of the gar in order to find regions of the genome containing developmentally relevant genes and their CREs. These genomic regions are then sequenced using next generation sequencing techniques. The results will potentially help us to understand the evolution of gene regulation in fish.accurate indicators of ancient local species distribution.

Molecular Evolution of Indian Hedgehog Following the Teleost Genome Duplication

Presenter : Ryan Loker

Mentor : Ingo Braasch

Major : Biology

Poster 26

Indian Hedgehog(IHH) is a signaling molecule that acts in several important developmental processes in vertebrates including gut, vascular, and skeletal development. Duplicated(paralogous) copies of the ihh gene have been retained in the teleost fish lineage, ihha and ihhb, following the teleost genome duplication(TGD). The mechanisms of evolution following a whole genome duplication are not completely understood, but one possible reason that ihh and many other duplicates remain in the teleost genomes is
that each paralog carries out essential sub-functions of the ancestral pre-duplication gene, following the Duplication-Degeneration-Complementation(DDC) model. Investigation of this mechanism requires characterization of the regulatory elements controlling expression of ihh genes in teleosts as well as the ancestral state, which can be represented using spotted gar(Lepisosteus oculatus), a member of a sister group to teleosts with an unduplicated genome. Here, we use a comparative genomics approach to compare the ge- nomes of several teleosts and gar in order to identify ancestral conserved non-coding elements(CNE) representing possible regulatory elements, and test their functionality in vivo using transgenic reporter constructs in zebrafish(Danio rerio). In addition to the insight of the evolutionary mechanisms, characterizing enhancers of ihha and ihhb will provide an opportunity to further characterize the role of these genes in developmental pathways, which are commonly conserved throughout vertebrates including humans.