DOI: 10.5061/dryad.7v1m1
title: Data from: The transcriptional landscape of seasonal coat colour moult in the snowshoe hare

description: 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 if 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
 non-model organisms can provide a crucial resource to dissect the genetic
 basis and evolution of complex seasonally changing traits.
description: Snowshoe hare skin
 transcriptome (raw)This transcriptome was
 assembled from 15 skin samples, collected from 5 adult snowshoe hares
 undergoing spring moult. From each of the 5 individuals, we collected 3
 skin biopsies in different moult stages and extracted mRNA. We produced
 strand specific cDNA libraries for each sample that we sequenced. We
 pooled read data for all samples and assembled this transcriptome using
 TRINITY.Lep_ame_raw_skin_transcriptome.Trinity.fastaSnowshoe hare skin transcriptome (filtered)This transcriptome was assembled from 15 skin samples, collected from 5 adult snowshoe hares undergoing spring moult. From each of the 5 individuals, we collected 3 skin biopsies in different moult stages and extracted mRNA. We produced strand specific cDNA libraries for each sample that we sequenced. We pooled read data for all samples and assembled this transcriptome using TRINITY. After assembling, we annotated the transcriptome to rabbit and mouse ENSEMBL protein database. Contigs that failed to annotate were removed from the transcriptome, resulting on this filtered version. We used this transcriptome to map reads and estimate expression values for each gene using RSEM.Lep_ame_filtered_skin_transcriptome.fastaSnowshoe hare gene level abundance estimations from RSEMThis tar file contains gene level results for 15 snowshoe hare skin samples. More information in the README file.Lep_ame_RSEM.out.genes.results.tarSnowshoe hare isoform level abundance estimations from RSEMThis tar file contains isoform level results for 15 snowshoe hare skin samples. More information in the README file.Lep_ame_RSEM.out.isoforms.results.tar