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

Abstract

We report here the successful assembly of the complete mitochondrial genomes of the northern spotted owl (<i>Strix occidentalis caurina</i>) and the barred owl (<i>S. varia</i>). 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 <i>S. o. caurina</i> and <i>S. varia</i> 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 <i>S. o. caurina</i> for copies of mitochondrial genes and found at least nine separate stretches of nuclear copies of gene sequences originating in the mitochondrial genome (<i>Numts</i>). The <i>Numts</i> ranged from 226-19,522 nt in length and included copies of all mitochondrial genes except <i>tRNA^Pro</i> , <i>ND6</i>, and <i>tRNA^Glu</i> . <i>Strix occidentalis caurina</i> and <i>S. varia</i> exhibited an average of 10.74% (8.68% uncorrected <i>p</i>-distance) divergence across the non-tRNA mitochondrial genes.