Evidence for a duplicated mitochondrial region in Audubon’s shearwater based on MinION sequencing

Abstract

Mitochondrial genetic markers have been extensively used to study the phylogenetics and phylogeography of many birds, including seabirds of the order Procellariiformes. Evidence suggests that part of the mitochondrial genome of Procellariiformes, especially albatrosses, is duplicated, but no DNA fragment covering the entire duplication has been sequenced. We sequenced the complete mitochondrial genome of a non-albatross species of Procellariiformes, Puffinus lherminieri (Audubon’s shearwater) using the long-read MinION (ONT) technology. Two mitogenomes were assembled from the same individual, differing by 52 SNPs and in length. The shorter was 19 kb long while the longer was 21 kb, due to the presence of two identical copies of nad6, three tRNA, and two dissimilar copies of the control region (CR). Contrary to albatrosses, cob was not duplicated. We further detected a complex repeated region of undetermined length between the CR and 12S. Long-read sequencing suggests heteroplasmy and a novel arrangement within the duplicated region, indicating a complex evolution of the mitogenome in Procellariiformes.

Keywords:

• Heteroplasmy
• control region
• long-range PCR
• tandem repeats
• cytochrome-b
• cytb

Acknowledgements

We thank the University of La Rochelle (ULR) for financial support, and the ULR molecular core facility for lab support. We thank Helen James and the National Museum of Natural History, Smithsonian Institution, for access to tissue sample USNM 620721; UCE data for this individual was originally gathered for an unpublished phylogenetics study of Procellariiformes conducted by AJW, RTC, Helen James, and VB. We are grateful to the bioinformatics platform Toulouse Midi-Pyrenees (Bioinfo GenoToul) for providing help and computing. We also thank C. Precheur, the Parc Naturel Regional de la Martinique and the DEAL Martinique for help and funding of the research program on the shearwater. Salary of LT is covered by a grant from the University of La Rochelle. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work is covered by a grant from the University of La Rochelle.