deNovo assembly and annotation of Ambystoma laterale and Ambystoma jeffersonianum transcriptomes: the first steps toward investigating polyploid salamander expression

Abstract

Polyploidy Ambystoma salamanders are interesting as stable polyploid vertebrate system. Polyploidy in vertebrates is not well understood, and the unique salamander complex features non-recombining genomes with varying levels of ploidy and contribution of parental species. We assembled and annotated the two major contributors to this complex, Ambystoma jeffersonianum and Ambystoma laterale in preparation for investigating how the genomes respond to diverse polyploidy. We assembled each transcriptome using four assemblers (Velvet, SOAPdeNOVO, Trinity, and TransAbyss). We then curated and annotated both transcriptomes using tr2aacds and Trinotate. Orthologs and differentially expressed genes between the two parental species were identified to establish a baseline by which to compare the polyploids. Additionally, we developed an immune inventory for the two transcriptomes. The annotation will be useful in the next steps as we investigate the polyploid salamander libraries to determine the effect of polyploidy on expression.