DOI: 10.5061/dryad.x0k6djhfh
title: Data from: Transcriptomic regulation of seasonal coat color change in hares

description: Color molts from summer brown to winter white coats have evolved in
 several species to maintain camouflage year-round in environments with
 seasonal snow. Despite the eco-evolutionary relevance of this key
 phenological adaptation, its molecular regulation has only recently begun
 to be addressed. Here, we analyze skin transcription changes during the
 autumn molt of the mountain hare (Lepus timidus) and integrate the results
 with an established model of gene regulation across the spring molt of the
 closely related snowshoe hare (L. americanus). We
 quantified differences in gene expression among three stages of
 molt progression – “brown” (early molt), “intermediate” and “white” (late
 molt). We found 632 differentially expressed genes, with a major pulse of
 expression early in the molt, followed by a milder one in late molt. The
 functional makeup of differentially expressed genes anchored the sampled
 molt stages to the developmental timeline of the hair growth cycle,
 associating anagen to early molt and the transition to catagen to late
 molt. The progression of color change was characterized by differential
 expression of genes involved in pigmentation, circadian and behavioral
 regulation. We found significant overlap between differentially expressed
 genes across the seasonal molts of mountain and snowshoe hares,
 particularly at molt onset, suggesting conservatism of gene regulation
 across species and seasons. However, some discrepancies suggest seasonal
 differences in melanocyte differentiation and the integration of
 nutritional cues. Our established regulatory model of seasonal coat color
 molt provides an important mechanistic context to study the functional
 architecture and evolution of this crucial seasonal adaptation.
description: To study the regulatory mechanisms underlying the autumn molt
 regulation (change from brown to white color), we collected skin samples
 representing three molt stages from four mountain hare individuals (4 x 3
 = 12 samples). We sequenced whole transcriptomes from each sample and
 analyzed the differences in expression between the three molt stages:
 early (brown hair), intermediate (brown and white hair) and late (white
 hair), using whole-transcriptome assembly, RSEM and edgeR. For the set of
 differentially expressed genes between molt stages we performed a Gene
 Ontology enrichment analysis using Ontologizer and a Reactome enrichment
 analysis. We build on previous results from snowshoe hares to construct a
 model on the regulation of seasonal coat color change. A description of
 the pipeline and scripts used can be found at
 https://github.com/evochange/coat_color_change_transcriptomics.
 Raw reads generated for this work are deposited at the Sequence
 Read Archive (SRA) under BioProject PRJNA590529.
description: Mountain hare skin transcriptome (raw) This
 transcriptome was assembled from 12 skin samples, collected in the Swiss
 Alps from 4 adult mountain hares undergoing autumn moult. From each of the
 4 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_tim_Alps_raw_transcriptome_trinity.Trinity.fasta
 Mountain hare skin transcriptome (Transrate "good"
 output) This transcriptome was assembled from 12 skin
 samples, collected in the Swiss Alps from 4 adult mountain hares
 undergoing autumn moult. From each of the 4 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 used Transrate to filter low quality contigs
 from the raw assembly. This file is the Transrate output.
 good.Lep_tim_Alps_transcriptome_trinity.Trinity.fasta
 Mountain hare transcriptome annotation (Transrate reciprocal
 blast output) We used Transrate's reciprocal
 blast feature to annotate the filtered mountain hare skin transcriptome to
 ENSEMBL 92 rabbit (OryCun2.0) and mouse (GRCm38.p6) protein
 references.
 good.APT_transcriptome_trinity.Trinity_into_Oryctolagus_cuniculus.OryCun2.0.pep.all.1<br> Oryctolagus_cuniculus.OryCun2.0.pep.all_into_good.APT_transcriptome_trinity.Trinity.2.blast<br> good.APT_transcriptome_trinity.Trinity_into_Mus_musculus.GRCm38.pep.all.1.blast<br> Mus_musculus.GRCm38.pep.all_into_good.APT_transcriptome_trinity.Trinity.2.blast Mountain hare gene and isoform level abundance estimations from RSEM This tar file contains gene and isoform level results from RSEM for 12 mountain hare skin samples. Bam files were mapped to the filtered mountain hare transcriptome generated in this work with Trinity and Transrate, using bowtie2. The bam files were used as input for RSEM. We filtered these results for multiple annotated genes as described in the methods section of the paper and in the GitHub evochange (https://github.com/evochange/coat_color_change_transcriptomics). Lep_tim_RSEM_gene_and_isoform_results.tar Raw reads generated for this work are deposited at the Sequence Read Archive (SRA) under BioProject PRJNA590529.<br> ​​​​​​More details on the pipeline followed and scripts used in this work can be found at https://github.com/evochange/coat_color_change_transcriptomics For any questions, please contact mafaldasferreira[at]cibio.up.pt