Purpose: To demonstrate that gene expression and splicing analysis varies considerably depending on the mapping reference genome. Methods: We mapped and analyzed submitted RNA reads using different tools and reference genomes to evaluate the influence of genome on DEG and alternative splicing tools. Results: We observed that these differences in transcriptome analysis are, in part, due to the presence of single nucleotide polymorphisms between the sequenced individual and each respective reference genome, as well as annotation differences between the reference genomes that exist even between syntenic orthologs. Conclusion: We conclude that even between two closely related genomes of similar quality, using the reference genome that is most closely related to the species being sampled significantly improves transcriptome. Overall design: Overall design: Using AM and PM timepoints, we anazyled DEG and alternative splicing to determine the affect of reference genome on analysis tools.