A mitochondrial long noncoding RNA in atlantic cod harbors complex heteroplasmic tandem repeat motifs

Abstract

A heteroplasmic tandem repeat (HTR) array occupies 100 to 300 bp of the mitochondrial DNA control region in the Atlantic cod, and recently we noted that the repeat appeared integrated in a polyadenylated mitochondrial long noncoding RNA. Here we provide a more detailed analysis of the mitochondrial HTR in the mitochondrial genome of 134 Atlantic cod specimens. We report all specimens to harbor mitochondrial HTRs in the control region, and identified 26 distinct variants among the 402 repeat motifs assessed. Whereas most specimens contained HTR profiles of 2–5 copies consisting of the same 40-bp motif, 22 specimens showed compound HTR arrays of at least two types of motifs present in the same mitochondrial DNA molecule. We found HTR profiles to be highly conserved between different tissue types of a single individual, and strictly maternally inherited in a mating experiment between parental Atlantic cod expressing different HTR profiles and array motifs. We conclude that mitochondrial heteroplasmy in the control region is very common in Atlantic cod, and results in length heterogenity of the long noncoding RNA lncCR-H.

Keywords:

• Atlantic cod
• heteroplasmy
• lncRNA
• mitogenome
• mtDNA

Acknowledgements

We thank Espen Olsen, Morten Krogstad, Espen Søreng, Ove Nicolaisen, Agnieszka Kijewska, Bill Hutchinson, Sherrylynn Rowe, Asgeir Aglen, and Francois Botha for the contribution of Atlantic cod specimen samples.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by grants from the Norwegian Research Council (GenoFisk), as well as Nord University and UiT – The Arctic University of Norway.