Isochore Diversity Across Nearly 300 Vertebrate Genomes Including a New Whiptail Lizard Genome

Hall, Alexander S.

Thermo Fisher Scientific

Houston, TX

alex.hall@thermofisher.com

Department of Biology

The University of Texas at Arlington

Arlington, TX

Baumann, Peter E.

Stowers Institute for Medical Research

Kansas City, MO

Howard Hughes Medical Institute

Kansas City, KS

Department of Molecular and Integrative Physiology

University of Kansas Medical Center

Kansas City, KS

Fujita, Matthew K.

Department of Biology

The University of Texas at Arlington

Arlington, TX

Vertebrate genome evolution has been studied most extensively in a small number of species. From these species, mostly mammalian, the foundational work was laid for broad scale patterns of genome content evolution. Importantly, isochores were discovered in these genomes: long (often >300 kbp) stretches of the genome with substantially similar GC content. From decades of study in the human and bovine genomes, five isochoric families have been identified and correlated with histone binding affinity, gene density, and recombination rates. But not all vertebrate genomes possess all or even more than one or two isochore families. In this study, we investigated broad scale genomic heterogeneity in four groups: fish, mammals, reptiles, and birds. Agreeing with previous work, these groups exhibit quite different GC content landscapes. The reasons for this are currently unknown and would benefit from a phylogenetically aware analysis. We also investigate isochore diversity in a smaller subset of genomes including an as-yet-unpublished whiptail lizard (Aspidoscelis marmoratus) genome assembly. This work confirmed recently contested results from the Anolis carolinensis genome that suggested some lizards lack isochore family diversity.


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