Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks

Huang, Yun, Chain, Frederic J. J., Panchal, Mahesh, Eizaguirre, Christophe, Kalbe, Martin, Lenz, Tobias L., Samonte, Irene E., Stoll, Monika, Bornberg-Bauer, Erich, Reusch, Thorsten B.H., Milinski, Manfred and Feulner, Philine G. D. (2016) Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks Molecular Ecology, 25 (4). pp. 943-958. DOI 10.1111/mec.13520.

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Text (Fig. S1 Distribution of dispersion values in (a) head kidney samples and (b) spleen samples)
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Text (Fig. S2 Counts of Diplostomum sp. across stickleback populations)
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Supplementary data:

Abstract

The observation of habitat-specific phenotypes suggests the action of natural selection. The three-spined stickleback (Gasterosteus aculeatus) has repeatedly colonized and adapted to diverse freshwater habitats across the northern hemisphere since the last glaciation, while giving rise to recurring phenotypes associated with specific habitats. Parapatric lake and river populations of sticklebacks harbour distinct parasite communities, a factor proposed to contribute to adaptive differentiation between these ecotypes. However, little is known about the transcriptional response to the distinct parasite pressure of those fish in a natural setting. Here, we sampled wild-caught sticklebacks across four geographical locations from lake and river habitats differing in their parasite load. We compared gene expression profiles between lake and river populations using 77 whole-transcriptome libraries from two immune-relevant tissues, the head kidney and the spleen. Differential expression analyses revealed 139 genes with habitat-specific expression patterns across the sampled population pairs. Among the 139 differentially expressed genes, eight are annotated with an immune function and 42 have been identified as differentially expressed in previous experimental studies in which fish have been immune challenged. Together, these findings reinforce the hypothesis that parasites contribute to adaptation of sticklebacks in lake and river habitats.

Document Type: Article
Additional Information: Data accessibility The raw reads of RNA-Seq data (fastq format) and mapping files (bam format) are available through the European Nucleotide Archive (study Accession no.: PRJEB8677, URL: http://www.ebi.ac.uk/ena/data/view/PRJEB8677). HTSEQ read counts, EDGER results and topGO results are archived in Dryad (doi:10.5061/ dryad.hq50s). Morphological and parasite data are included in Table S1 (Supporting information) - WOS:000370653700009; PubMed ID: 26749022
Keywords: habitat-specific gene expression; immune genes; parasites; RNA-Seq; three-spined stickleback; transcriptomics
Research affiliation: OceanRep > GEOMAR > FB3 Marine Ecology > FB3-EV Evolutionary Ecology of Marine Fishes
Kiel University
Refereed: Yes
DOI etc.: 10.1111/mec.13520
ISSN: 0962-1083
Related URLs:
Date Deposited: 19 Feb 2016 09:04
Last Modified: 03 May 2017 07:34
URI: http://eprints.uni-kiel.de/id/eprint/31419

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