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Data from: Transcriptomic regulation of seasonal coat color change in hares

Citation

Sousa Ferreira, Mafalda et al. (2020), Data from: Transcriptomic regulation of seasonal coat color change in hares, Dryad, Dataset, https://doi.org/10.5061/dryad.x0k6djhfh

Abstract

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.

Methods

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.

Usage Notes

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
Oryctolagus_cuniculus.OryCun2.0.pep.all_into_good.APT_transcriptome_trinity.Trinity.2.blast
good.APT_transcriptome_trinity.Trinity_into_Mus_musculus.GRCm38.pep.all.1.blast
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.
​​​​​​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

 

Funding

Fundação para a Ciência e a Tecnologia, Award: PTDC/BIA-EVF/1624/2014

National Science Foundation, Award: OIA-1736249

Fundação para a Ciência e a Tecnologia, Award: PD/BD/108131/2015

Fundação para a Ciência e a Tecnologia, Award: IF/00033/2014/CP1256/CT0005

National Science Foundation, Award: DEB-1907022

European Union's Seventh Framework Programme, Award: 286431

M.J. Murdock Charitable Trust, Award: Montana Genomics Core

National Institutes of Health, Award: S10RR029668, S10RR027303

Agence Nationale de la Recherche, Award: ANR-10-LABX-04-01A

Fundação Luso-Americana para o Desenvolvimento, Award: Portugal-United States of America Research Networks Program