Northern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light-Associated Genes

Zachary R Hanna; James B Henderson; Jeffrey D Wall; Christopher A Emerling; Jérôme Fuchs; Charles Runckel; David P Mindell; Rauri C K Bowie; Joseph L DeRisi; John P Dumbacher

doi:10.1093/gbe/evx158

Northern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light-Associated Genes

Genome Biol Evol. 2017 Oct 1;9(10):2522-2545. doi: 10.1093/gbe/evx158.

Authors

Zachary R Hanna^{1

2

3

4}, James B Henderson^{3

4}, Jeffrey D Wall^{1

3

4

5}, Christopher A Emerling^{1

2}, Jérôme Fuchs^{3

6}, Charles Runckel^{7

8

9}, David P Mindell¹, Rauri C K Bowie^{1

2}, Joseph L DeRisi^{7

8}, John P Dumbacher^{3

4}

Affiliations

¹ Museum of Vertebrate Zoology, University of California, Berkeley, California, USA.
² Department of Integrative Biology, University of California, Berkeley, California, USA.
³ Department of Ornithology & Mammalogy, California Academy of Sciences, San Francisco, California, USA.
⁴ Center for Comparative Genomics, California Academy of Sciences, San Francisco, California, USA.
⁵ Institute for Human Genetics, University of California, San Francisco, California, USA.
⁶ UMR 7205 Institut de Systématique, Evolution, Biodiversité, CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France.
⁷ Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA.
⁸ Howard Hughes Medical Institute, Bethesda, Maryland, USA.
⁹ Runckel & Associates, Portland, Oregon, USA.

Abstract

We report here the assembly of a northern spotted owl (Strix occidentalis caurina) genome. We generated Illumina paired-end sequence data at 90× coverage using nine libraries with insert lengths ranging from ∼250 to 9,600 nt and read lengths from 100 to 375 nt. The genome assembly is comprised of 8,108 scaffolds totaling 1.26 × 109 nt in length with an N50 length of 3.98 × 106 nt. We calculated the genome-wide fixation index (FST) of S. o. caurina with the closely related barred owl (Strix varia) as 0.819. We examined 19 genes that encode proteins with light-dependent functions in our genome assembly as well as in that of the barn owl (Tyto alba). We present genomic evidence for loss of three of these in S. o. caurina and four in T. alba. We suggest that most light-associated gene functions have been maintained in owls and their loss has not proceeded to the same extent as in other dim-light-adapted vertebrates.

Keywords: Aves; Strigidae; Strigiformes; bird; nuclear genome.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Birds / genetics
Genome*
Genome, Mitochondrial
Light
Molecular Sequence Annotation
Strigiformes / classification*
Strigiformes / genetics*
Vision, Ocular

Abstract

Publication types

MeSH terms

Grants and funding