The Origins and Evolution of Chromosomes and the Recombination Landscape in Rattlesnake Genomes

Schield, Drew R.

dschield@uta.edu

Perry, Blair W.

Department of Biology

University of Texas at Arlington Arlington, Texas, USA

Smith, Cara F.

School of Biological Sciences

University of Northern Colorado Greeley, Colorado, USA

Meik, Jesse M.

Department of Biological Sciences Tarleton State University

Stephenville, Texas, USA

Mackessy, Stephen P.

School of Biological Sciences

University of Northern Colorado

Greeley, Colorado, USA

Castoe, Todd A. Department of Biology

University of Texas at Arlington

Arlington, Texas, USA

For years, the quality of reptile genomes has lagged behind those of mammals and birds, but new molecular techniques have made highly-contiguous genomes from non-model organisms possible. Here we present a chromosome-level genome assembly of the prairie rattlesnake (Crotalus viridis viridis), which we used to study key features of genome biology and evolution in reptiles. We identify the rattlesnake Z chromosome, including the recombining pseudoautosomal region, and find evidence for partial dosage compensation driven by an evolutionary accumulation of a female-biased upregulation mechanism. Comparative analyses with other amniotes provide new insight into the origins, structure, and function of reptile microchromosomes, which we demonstrate have markedly different structure and function compared to macrochromosomes. Snake microchromosomes are also enriched for venom genes, which we show have evolved through multiple tandem duplication events in multiple gene families. We further leverage this genome in combination with whole genome re-sequencing data from populations to characterize the recombination landscape in snakes for the first time, which further illustrate the unique aspects of microchromosomes and their evolutionary significance. Our findings reveal novel and fundamental features of reptile genome biology, provide insight into the regulation of snake venom, and broadly highlight the biological insight enabled by chromosome-level genome assemblies.


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