Environmental Biology of Fishes

, Volume 101, Issue 5, pp 711–721 | Cite as

Unmapped sequencing reads identify additional candidate genes linked to magnetoreception in rainbow trout

  • Monica B. Arniella
  • Robert R. Fitak
  • Sönke Johnsen


A recent study identified candidate genes linked to magnetoreception in rainbow trout (Oncorhynchus mykiss) by sequencing transcriptomes from the brains of fish exposed to a magnetic pulse. However, the discovery of these candidate genes was limited to sequences that aligned to the reference genome. The unaligned, or unmapped, sequences may yet contain valuable information resulting from regions missing, misassembled, or divergent from the reference. Using the available sequencing data from the trout brain transcriptomes, we assembled >27 million unmapped sequences (5.8% of total sequences) into 45,142 contigs and identified 12 differentially expressed contigs as a result of exposure to a pulsed magnetic field. These contigs encoded a putative superoxide dismutase – a protein necessary to prevent oxidative damage – and collagen alpha-1 type II – a structural protein important for the development and integrity of the retina. These genes were consistent with the previous study suggesting an effect of the magnetic pulse on oxidative consequences of free iron and on non-visual encephalic photoreceptors. Our results demonstrate the utility of assembling unmapped sequencing reads in studies of gene expression and identify additional candidate genes associated with a magnetic sense in trout.


Gene expression Transcriptomics RNA-seq Oncorhynchus mykiss 



We would like to thank the Duke Shared Cluster Resource for providing the computational resources necessary for the project. We also thank E. Caves, L. Schweikert, and J. Notar for comments on earlier drafts of this manuscript. This work was supported by the Duke University Scholars Program [to M.B.A.] and the Air Force Office of Scientific Research [FA9550-14-1-0208 to S.J. and R.R.F].

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.


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© Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  • Monica B. Arniella
    • 1
  • Robert R. Fitak
    • 1
  • Sönke Johnsen
    • 1
  1. 1.Department of BiologyDuke UniversityDurhamUSA

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