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PeerJ. 2017 Oct 10;5:e3901. doi: 10.7717/peerj.3901. eCollection 2017.

Complete mitochondrial genome sequences of the northern spotted owl (Strix occidentalis caurina) and the barred owl (Strix varia; Aves: Strigiformes: Strigidae) confirm the presence of a duplicated control region.

Author information

1
Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America.
2
Department of Integrative Biology, University of California, Berkeley, CA, United States of America.
3
Department of Ornithology & Mammalogy, California Academy of Sciences, San Francisco, CA, United States of America.
4
Center for Comparative Genomics, California Academy of Sciences, San Francisco, CA, United States of America.
5
Chan Zuckerberg Biohub, San Francisco, CA, United States of America.
6
UMR 7205 Institut de Systématique, Evolution, Biodiversité, CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France.

Abstract

We report here the successful assembly of the complete mitochondrial genomes of the northern spotted owl (Strix occidentalis caurina) and the barred owl (S. varia). We utilized sequence data from two sequencing methodologies, Illumina paired-end sequence data with insert lengths ranging from approximately 250 nucleotides (nt) to 9,600 nt and read lengths from 100-375 nt and Sanger-derived sequences. We employed multiple assemblers and alignment methods to generate the final assemblies. The circular genomes of S. o. caurina and S. varia are comprised of 19,948 nt and 18,975 nt, respectively. Both code for two rRNAs, twenty-two tRNAs, and thirteen polypeptides. They both have duplicated control region sequences with complex repeat structures. We were not able to assemble the control regions solely using Illumina paired-end sequence data. By fully spanning the control regions, Sanger-derived sequences enabled accurate and complete assembly of these mitochondrial genomes. These are the first complete mitochondrial genome sequences of owls (Aves: Strigiformes) possessing duplicated control regions. We searched the nuclear genome of S. o. caurina for copies of mitochondrial genes and found at least nine separate stretches of nuclear copies of gene sequences originating in the mitochondrial genome (Numts). The Numts ranged from 226-19,522 nt in length and included copies of all mitochondrial genes except tRNAPro , ND6, and tRNAGlu . Strix occidentalis caurina and S. varia exhibited an average of 10.74% (8.68% uncorrected p-distance) divergence across the non-tRNA mitochondrial genes.

KEYWORDS:

Barred owl; Bird; Control region; Mitochondrial genome; Mtgenome; Northern spotted owl; mtDNA

Conflict of interest statement

The authors declare there are no competing interests.

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