Background: The cotton rat (Sigmodon) is the gold standard pre-clinical animal model for respiratory viral pathogens, especially for Respiratory Syncytial Virus (RSV). However, without a published genome, transcriptomic analysis in cotton rats is not possible. The aim of this study was to generate a comprehensive de novo transcriptome from multiple organs of two species of cotton rats commonly used in the laboratory (S. fulviventer and S. hispidus) and compare and contrast lung gene expression and immune response changes between the two species upon RSV infection.
Results: Our assembly generated nearly 120,000 gene and isoform annotations for each species. Following RSV infection, we identified 279 unique and annotated genes to be up- and down-regulated, including several genes strongly implicated in RSV infection (Mx1, I27L2, IIGP1, LY6E, Viperin, Keratin 6A) as well as novel genes not previously described in RSV research (LG3BP, SYWC, MYO7B, A1CF, APOBEC1, RIC1, KPYR, Claudin-2, and NR1H4)
Conclusions: This study presents transcriptome references for future RNA-seq studies in the cotton rat model, as well as provides gene sequences for molecular diagnostics during research. Our differential expression analysis highlights potential targets for RSV pathogenesis, treatment, and prevention. Less...