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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

, , , , ,
1 Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, United States of America
2 Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
3 Department of Ornithology & Mammalogy, California Academy of Sciences, San Francisco, California, United States of America
4 Center for Comparative Genomics, California Academy of Sciences, San Francisco, California, United States of America
5 Chan Zuckerberg Biohub, San Francisco, California, United States of America
6 UMR 7205 Institut de Systématique, Evolution, Biodiversité, CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Département Systématique et Evolution, Muséum National d’Histoire Naturelle, Paris, France
DOI
10.7287/peerj.preprints.3120v1
Published
Accepted
Subject Areas
Genetics, Genomics, Molecular Biology, Zoology
Keywords
mitochondrial genome, bird, northern spotted owl, barred owl, mtGenome, mtDNA, control region
Copyright
© 2017 Hanna et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Hanna ZR, Henderson JB, Sellas AB, Fuchs J, Bowie RCK, Dumbacher JP. 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. PeerJ Preprints 5:e3120v1

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 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. 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).

Author Comment

This is a submission to PeerJ for review.

Supplemental Information

Supplementary Materials

Supplementary details of methodology

DOI: 10.7287/peerj.preprints.3120v1/supp-1

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Zachary R Hanna conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

James B Henderson conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Anna B Sellas conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Jérôme Fuchs conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.

Rauri C. K. Bowie conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

John P Dumbacher conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

Complete mitochondrial genome sequence of Strix occidentalis caurina CAS:ORN:98821 deposited as NCBI GenBank Accession MF431746.

Complete mitochondrial genome sequence of Strix varia varia CMC:ORNI-T:B41533 deposited as NCBI GenBank Accession MF431745.

Data Deposition

The following information was supplied regarding data availability:

Specimen Sequoia blood sample deposited as CAS:ORN:98821, California Academy of Sciences, San Francisco, California, United States of America.

BLATq deposited at Zenodo DOI: 10.5281/zenodo.61136 and available at <https://github.com/calacademy-research/blatq>.

excerptByIDs deposited at Zenodo DOI: 10.5281/zenodo.61134 and available at <https://github.com/calacademy-research/excerptByIDs>.

Funding

Funds provided by Michael and Katalina Simon (to J.P.D.); the Louise Kellogg Fund, Museum of Vertebrate Zoology, University of California, Berkeley (to Z.R.H.); and the National Science Foundation Graduate Research Fellowship (DGE 1106400 to Z.R.H.) made this work possible. Any opinion, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation. This work used data produced by the Vincent J. Coates Genomics Sequencing Laboratory at the University of California, Berkeley, supported by NIH S10 Instrumentation Grants (S10 RR029668, S10 RR027303). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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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
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