The transcriptional landscape of seasonal coat colour moult in the snowshoe hare

Abstract

Seasonal coat colour change is an important adaptation to seasonally changing environments but the evolution of this and other circannual traits remains poorly understood. In this study, we use gene expression to understand seasonal coat colour moulting in wild snowshoe hares (Lepus americanus). We used hair colour to follow the progression of the moult, simultaneously sampling skin from three moulting stages in hares collected during the peak of the spring moult from white winter to brown summer pelage. Using RNA sequencing, we tested whether patterns of expression were consistent with predictions based on the established phases of the hair growth cycle. We found functionally consistent clustering across skin types, with 766 genes differentially expressed between moult stages. "White" pelage showed more differentially expressed genes that were upregulated relative to other skin types, involved in the transition between late telogen (quiescent stage) and the onset of anagen (proliferative stage). Skin samples from transitional "intermediate" and "brown" pelage were transcriptionally similar and resembled the regressive transition to catagen (regressive stage). We also detected differential expression of several key circadian clock and pigmentation genes, providing important means to dissect the bases of alternate seasonal colour morphs. Our results reveal that pelage colour is a useful biomarker for seasonal change but that there is a consistent lag between the main gene expression waves and change in visible coat colour. These experiments establish that developmental sampling from natural populations of nonmodel organisms can provide a crucial resource to dissect the genetic basis and evolution of complex seasonally changing traits.

Transcriptomic regulation of seasonal coat color change in hares

“…The 3‐individuals’ dataset provided higher power (0.82 vs. 0.72 to detect a 1.5‐fold change for a probability of false positives of 0.05) and lower BCV (0.16 vs. 0.21) when compared to the 4‐individuals’ dataset. This estimated power is comparable to that of the snowshoe hare dataset from Ferreira et al, () (0.85 to detect 1.5‐fold changes in expression), and adequate to detect differential expression for lowly expressed genes (Todd, Black, & Gemmell, ). Therefore, hereafter we report the results from the analyses of the 3‐individuals’ dataset.…”

“…The inspection of the MDS plot revealed that the skin samples of one individual consistently deviated from the remaining samples and did not capture the individualization of the sampled molt stages aimed with our sampling strategy (Figure ) (Ferreira et al, ). This suggests an artificial bias during sampling that increased the variance in the dataset.…”

“…Furthermore, 10 Reactome pathways were found enriched in cluster 1, 18 in cluster 2 and 9 in cluster 3 (Figure b, Tables –). In general, the enrichment analysis revealed functions and pathways that are expected in the molting skin (Ferreira et al, ). Both clusters with higher levels of expression in “brown” (1 and 2; Figure b) showed a similar enrichment of GO terms that were related with muscle development, cytoskeleton organization, transmembrane transport, circulatory system development, cell–cell communication and adhesion and regulation of gene expression and protein synthesis (Figure b, Tables and ).…”

“…A de novo skin transcriptome assembly for L. timidus was performed to allow an independent unbiased comparison with the results of Ferreira et al, (). The transcriptome assembly was performed with Trinity (2.6.6) (Grabherr et al, ), using filtered and properly paired reads and specifying “RF” for strand‐specific assembly.…”

“…However, the specific regulatory mechanisms of coat color changing molts have only been addressed recently. We previously studied the regulatory patterns of seasonal changing molts in snowshoe hares, inferring gene expression changes in the skin during the spring white‐to‐brown molt in the species using RNA‐sequencing (Ferreira et al, ). This work established a genic regulatory model for the seasonal molt of snowshoe hares characterized primarily by genes involved in the hair growth cycle, circadian rhythms, and pigmentation.…”