Uncovering the Molecular Mechanisms of Stripe Pattern Formation in Thirteen-Lined Ground Squirrels

Abstract

Animal periodic color patterns, such as zebra stripes or leopard spots, represent some of nature’s most distinguishable phenotypes. In rodents, periodic pigment patterns have independently evolved in species from distantly related families, a classic example of convergent evolution (the independent acquisition of similar traits). A previous study identified a set of genes and regulatory elements implicated in patterning the stripes of African striped mice (Rhabdomys pumilio) during development. However, it remains unknown whether these mechanisms are unique to the African striped mouse or are also responsible for patterning the stripes of other rodents. Here, I have investigated this question by first performing transcriptomic analyses of different skin regions of the thirteen-lined ground squirrel (Spermophilus tridecemlineatus), a rodent with a pattern consisting of alternating dark and tan stripes with a line of tan spots in each dark stripe. Using RNA-seq, I identified 38 genes that are differentially expressed between stripes, including known pigmentation genes such as Asip and Edn3. Second, using a novel chromatin-profiling approach, I have identified two categories of genomic regions that may regulate differential gene expression in the TLGS. Together, these results reveal the main transcriptomic and regulatory regions underlying stripe formation in the TLGS and suggest that, although some mechanisms of stripe formation are shared between the African striped mouse and the TLGS, there are multiple ways in which similar phenotypes can be specified at the molecular level.