Northern Spotted Owl (Strix Occidentalis Caurina) Genome: Divergence with the Barred Owl (Strix Varia) and Characterization of Light-Associated Genes

Overview

Journal Genome Biol Evol

Publisher Oxford University Press

Specialties Biology
Genetics
Molecular Biology

Date 2017 Oct 10

PMID 28992302

Citations 14

Authors

Zachary R Hanna

James B Henderson

Jeffrey D Wall

Christopher A Emerling

Jerome Fuchs

Charles Runckel

David P Mindell

Rauri C K Bowie

Joseph L DeRisi

John P Dumbacher

Affiliations

Soon will be listed here.

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.

Citing Articles

Chromosome-level reference genome assembly of the gyrfalcon (Falco rusticolus) and population genomics offer insights into the falcon population in Mongolia.

Al-Ajli F, Formenti G, Fedrigo O, Tracey A, Sims Y, Howe K Sci Rep. 2025; 15(1):4154.

PMID: 39900672 PMC: 11790892. DOI: 10.1038/s41598-025-88216-9.

Repeated evolution on oceanic islands: comparative genomics reveals species-specific processes in birds.

Recuerda M, Montoya J, Blanco G, Mila B BMC Ecol Evol. 2024; 24(1):140.

PMID: 39516810 PMC: 11545622. DOI: 10.1186/s12862-024-02320-4.

Revealing the Demographic History of the European Nightjar ().

Day G, Fox G, Hipperson H, Maher K, Tucker R, Horsburgh G Ecol Evol. 2024; 14(10):e70460.

PMID: 39463738 PMC: 11512156. DOI: 10.1002/ece3.70460.

Evolution of visual guanylyl cyclases and their activating proteins with respect to clade and species-specific visual system adaptation.

Gesemann M, Neuhauss S Front Mol Neurosci. 2023; 16:1131093.

PMID: 37008786 PMC: 10061024. DOI: 10.3389/fnmol.2023.1131093.

An efficient exact algorithm for identifying hybrids using population genomic sequences.

Chakraborty S, Rannala B Genetics. 2023; 223(4).

PMID: 36708142 PMC: 10078916. DOI: 10.1093/genetics/iyad011.

References

Warren W, Hillier L, Tomlinson C, Minx P, Kremitzki M, Graves T . A New Chicken Genome Assembly Provides Insight into Avian Genome Structure. G3 (Bethesda). 2016; 7(1):109-117. PMC: 5217101. DOI: 10.1534/g3.116.035923. View

Le Duc D, Renaud G, Krishnan A, Almen M, Huynen L, Prohaska S . Kiwi genome provides insights into evolution of a nocturnal lifestyle. Genome Biol. 2015; 16:147. PMC: 4511969. DOI: 10.1186/s13059-015-0711-4. View

ROTH J, Gern W, Roth E, Ralph C, Jacobson E . Nonpineal melatonin in the alligator (Alligator mississippiensis). Science. 1980; 210(4469):548-50. DOI: 10.1126/science.7423204. View

Heesy C, Hall M . The nocturnal bottleneck and the evolution of mammalian vision. Brain Behav Evol. 2010; 75(3):195-203. DOI: 10.1159/000314278. View

Mundy N, Stapley J, Bennison C, Tucker R, Twyman H, Kim K . Red Carotenoid Coloration in the Zebra Finch Is Controlled by a Cytochrome P450 Gene Cluster. Curr Biol. 2016; 26(11):1435-40. DOI: 10.1016/j.cub.2016.04.047. View

Yates A, Akanni W, Amode M, Barrell D, Billis K, Carvalho-Silva D . Ensembl 2016. Nucleic Acids Res. 2015; 44(D1):D710-6. PMC: 4702834. DOI: 10.1093/nar/gkv1157. View

Tariq Mahmood M, McLenachan P, Gibb G, Penny D . Phylogenetic position of avian nocturnal and diurnal raptors. Genome Biol Evol. 2014; 6(2):326-32. PMC: 3942033. DOI: 10.1093/gbe/evu016. View

Bao W, Kojima K, Kohany O . Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob DNA. 2015; 6:11. PMC: 4455052. DOI: 10.1186/s13100-015-0041-9. View

Soni B, Foster R . A novel and ancient vertebrate opsin. FEBS Lett. 1997; 406(3):279-83. DOI: 10.1016/s0014-5793(97)00287-1. View

10.

Tarttelin E, Bellingham J, Bibb L, Foster R, Hankins M, Gregory-Evans K . Expression of opsin genes early in ocular development of humans and mice. Exp Eye Res. 2003; 76(3):393-6. DOI: 10.1016/s0014-4835(02)00300-7. View

11.

Nakamura D, Tiersch T, Douglass M, Chandler R . Rapid identification of sex in birds by flow cytometry. Cytogenet Cell Genet. 1990; 53(4):201-5. DOI: 10.1159/000132930. View

12.

Verra D, Contin M, Hicks D, Guido M . Early onset and differential temporospatial expression of melanopsin isoforms in the developing chicken retina. Invest Ophthalmol Vis Sci. 2011; 52(8):5111-20. DOI: 10.1167/iovs.11-75301. View

13.

Simoes B, Sampaio F, Jared C, Antoniazzi M, Loew E, Bowmaker J . Visual system evolution and the nature of the ancestral snake. J Evol Biol. 2015; 28(7):1309-20. DOI: 10.1111/jeb.12663. View

14.

Emerling C . Independent pseudogenization of CYP2J19 in penguins, owls and kiwis implicates gene in red carotenoid synthesis. Mol Phylogenet Evol. 2017; 118:47-53. DOI: 10.1016/j.ympev.2017.09.016. View

15.

Falcon J, Besseau L, Fuentes M, Sauzet S, Magnanou E, Boeuf G . Structural and functional evolution of the pineal melatonin system in vertebrates. Ann N Y Acad Sci. 2009; 1163:101-11. DOI: 10.1111/j.1749-6632.2009.04435.x. View

16.

Bowmaker J, Martin G . Visual pigments and colour vision in a nocturnal bird, Strix aluco (tawny owl). Vision Res. 1978; 18(9):1125-30. DOI: 10.1016/0042-6989(78)90095-0. View

17.

Wu Y, Hadly E, Teng W, Hao Y, Liang W, Liu Y . Retinal transcriptome sequencing sheds light on the adaptation to nocturnal and diurnal lifestyles in raptors. Sci Rep. 2016; 6:33578. PMC: 5028738. DOI: 10.1038/srep33578. View

18.

Wicker T, Robertson J, Schulze S, Feltus F, Magrini V, Morrison J . The repetitive landscape of the chicken genome. Genome Res. 2004; 15(1):126-36. PMC: 540276. DOI: 10.1101/gr.2438004. View

19.

Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J . SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience. 2013; 1(1):18. PMC: 3626529. DOI: 10.1186/2047-217X-1-18. View

20.

Guan X, Xu J, Smith E . The complete mitochondrial genome sequence of the budgerigar, Melopsittacus undulatus. Mitochondrial DNA A DNA Mapp Seq Anal. 2014; 27(1):401-2. DOI: 10.3109/19401736.2014.898277. View