Mitochondrial genome diversity among six laboratory zebrafish (Danio rerio) strains

Abstract

The mitochondrial genome (mtDNA) is distinct from the nuclear genome and is known to play a significant role in several disease phenotypes, such as longevity and fertility. Here we characterize the complete mitochondrial genomes (∼16 590 bp), and the extent of within and between strain variation for 27 adult zebrafish, representing five commonly used laboratory strains (AB, TL, HL, WIK, and SJD) and one line acquired from a local pet shop. These data were subsequently analyzed to determine the phylogenetic relationships between strains and ascertain if positive selection might be operating on any mtDNA genes. Relationships between strains are not entirely consistent with those observed previously using nuclear DNA. Further there is a substantial body of variation within current zebrafish lines, with 172 variants described across lines. Of these, 27 changes are non-synonymous and there is nominal evidence for positive selection in the mtDNA sequences at some of these sites. We further identify novel frameshift mutations in eight genes, which are all predicted to have functional consequences. Our study provides the first information on mtDNA diversity in zebrafish, identifies multiple non-synonymous substitutions and other mutations expected to have functional effects, and represents an important first step in establishing zebrafish as a model for investigating the phenotypic effects of mtDNA mutations.

Keywords:

• Disease
• genetic variation
• mtDNA
• mutation
• phenotype
• positive selection

Acknowledgements

The authors thank Edwin Cuppen (Hubrecht Research Institution) for zebrafish DNAs and the University of Otago Zebrafish facility for logistic support. They also thank Janine Wing, Joanne Gillum, and the University of Otago Genetic Analysis Service for technical support.

Declaration of interest

The authors report that they have no conflicts of interests. This work was supported by funds from the University of Otago to N. J. G. and the Dean’s Prestigious Summer Scholarship to B. S.

Supplementary material available online