Transcriptomic regulation of seasonal coat color change in hares
Creators
- 1. CIBIO/InBIO, University of Porto
- 2. CIBIO/InBIO, University of Porto, University of Montana
- 3. University of Montana
- 4. Landesforschungsanstalt für Landwirtschaft und Fischerei
- 5. University of Natural Resources and Life Sciences
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.
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.
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 provided by: Fundação para a Ciência e a Tecnologia
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001871
Award Number: PTDC/BIA-EVF/1624/2014
Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: OIA-1736249
Funding provided by: Fundação para a Ciência e a Tecnologia
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001871
Award Number: PD/BD/108131/2015
Funding provided by: Fundação para a Ciência e a Tecnologia
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001871
Award Number: IF/00033/2014/CP1256/CT0005
Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: DEB-1907022
Funding provided by: European Union's Seventh Framework Programme
Crossref Funder Registry ID:
Award Number: 286431
Funding provided by: M.J. Murdock Charitable Trust
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000937
Award Number: Montana Genomics Core
Funding provided by: National Institutes of Health
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000002
Award Number: S10RR029668, S10RR027303
Funding provided by: Agence Nationale de la Recherche
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001665
Award Number: ANR-10-LABX-04-01A
Funding provided by: Fundação Luso-Americana para o Desenvolvimento
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100007472
Award Number: Portugal-United States of America Research Networks Program
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Additional details
Related works
- Is cited by
- 10.1111/mec.14177 (DOI)