title: Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks.
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.
authors.affiliation: Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.
authors.forename: Yun
authors.initials: Y
authors.lastname: Huang
authors.affiliation: Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.|Department of Biology, McGill University, Montreal, QC, Canada, H3A 1B1.
authors.forename: Frédéric J J
authors.initials: FJ
authors.lastname: Chain
authors.affiliation: Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.|Bioinformatics Infrastructures for Life Sciences (BILS), Uppsala Biomedicinska Centrum (BMC), Husargatan 3, 751 23, Uppsala, Sweden.|Institute of Medical Biochemistry and Microbiology, Uppsala Biomedicinska Centrum (BMC), Husargatan 3, 751 23, Uppsala, Sweden.
authors.forename: Mahesh
authors.initials: M
authors.lastname: Panchal
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London, E1 4NS, London, UK.
authors.forename: Christophe
authors.initials: C
authors.lastname: Eizaguirre
authors.affiliation: Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Kalbe
authors.affiliation: Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.
authors.forename: Tobias L
authors.initials: TL
authors.lastname: Lenz
authors.affiliation: Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.
authors.forename: Irene E
authors.initials: IE
authors.lastname: Samonte
authors.affiliation: Institute of Human Genetics, Genetic Epidemiology, Westfälische Wilhelms University, 48149, Münster, Germany.
authors.forename: Monika
authors.initials: M
authors.lastname: Stoll
authors.affiliation: Institute for Evolution and Biodiversity, Evolutionary Bioinformatics, Westfälische Wilhelms University, 48149, Münster, Germany.
authors.forename: Erich
authors.initials: E
authors.lastname: Bornberg-Bauer
authors.affiliation: Evolutionary Ecology of Marine Fishes, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24105, Kiel, Germany.
authors.forename: Thorsten B H
authors.initials: TB
authors.lastname: Reusch
authors.affiliation: Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.
authors.forename: Manfred
authors.initials: M
authors.lastname: Milinski
authors.affiliation: Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.|Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047, Kastanienbaum, Switzerland.
authors.forename: Philine G D
authors.initials: PG
authors.lastname: Feulner
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D000818:Animals; D002170:Canada; D017753:Ecosystem; D060146:Ecotype; D020869:Gene Expression Profiling; D005828:Genetics, Population; D005858:Germany; D060106:Lakes; D009664:Norway; D045483:Rivers; D017423:Sequence Analysis, RNA; D023701:Smegmamorpha / Q000235:genetics* / Q000276:immunology / Q000469:parasitology; D059467:Transcriptome
keywords: RNA-Seq; habitat-specific gene expression; immune genes; parasites; three-spined stickleback; transcriptomics