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

Huang, Yun; Chain, Frédéric 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; Feulner, Philine (2016). Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks. Molecular Ecology, 25(4), pp. 943-958. Wiley-Blackwell 10.1111/mec.13520

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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 commu-
nities, a factor proposed to contribute to adaptive differentiation between these eco-
types. 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 stick-
lebacks across four geographical locations from lake and river habitats differing in
their parasite load. We compared gene expression profiles between lake and river pop-
ulations 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.

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