Evolution of Genome Structure

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Mammals and birds have large genomic regions with elevated GC-content.  These regions, called, isochores, correlate with several fundamental features, including gene density, recombination rate, substitution rate, and repeat landscape.  Because of this, isochores themselves have been considered fundamental genomic structures.  The availability of the Anolis carolinensis genome allows us, for the first time, to explicitly examine isochore structure in a non-avian reptile.

We could not find any evidence for GC-rich isochores in Anolis.  Because of the flat GC landscape of the Anolis genome, we could not find associations with gene density or intron length with GC content, typical correlates that are strong in mammals and birds.  

What may have caused the homogenization of GC-content in Anolis?  One of the main hypotheses driving isochore evolution is that a recombination-based mechanism, GC-biased gene conversion, is strong enough to overwhelm an AT-mutation bias, and lead to increased substitutions to G and C.  Consistent with our results, Anolis also has a more homogeneous recombination landscape than human and chicken.  However, we cannot rule out the possibilities that Anolis (1) lacks GC-biased gene conversion, or (2) the ancestral effective population size of Anoliswas so small so as to reduce the efficiency of GC-biased gene conversion.

Our lab is continuing our investigation of isochore and genome structure in amniotes in collaboration with several other investigators.  For example, we will be working closely with Dr. Todd Castoe and his lab in investigationg the evolutionary genomics of reptiles and amphibians.

© Matthew Fujita 2012