Genome sequencing and transcriptome analysis of the phenotypically plastic spadefoot toads

Frogs and toads (anurans) are widely used to study many biological problems, however, few have genome assemblies or annotations. This lack of resources limits the possible research that can be conducted in these systems. Research strategies that are commonplace in many systems, such as genome wide association studies or quantitative trait mapping, are not feasible without a reference. However, thanks to the continuing reduction in the cost of sequencing, it has become possible for small lab groups to generate high quality genomes and annotations for their model of choice. In chapter two I describe the genome sequencing, assembly, and annotation of a promising anuran system as well as limited biological insight into some of its attributes. In chapter three I describe a transcriptomic analysis of inter species hybrids in this system enabled by the genome described in chapter two. This transcriptomic analysis revealed large-scale patterns of differential expression unique to hybrids consistent with reinforcement of hybrid boundaries.