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

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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 × 10 ⁹ nt in length with an N50 length of 3.98 × 10 ⁶ nt. We calculated the genome-wide fixation index ( F _ST) 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.

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Repbase update: a database and an electronic journal of repetitive elements.

J Jurka (2000)

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Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

, , … (2013)

Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results - In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions - Many current genome assemblers produced useful assemblies, containing a significant representation of their genes, regulatory sequences, and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.

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PyEvolve: a toolkit for statistical modelling of molecular evolution

Andrew Butterfield, Vivek Vedagiri, Edward Lang … (2004)

Background Examining the distribution of variation has proven an extremely profitable technique in the effort to identify sequences of biological significance. Most approaches in the field, however, evaluate only the conserved portions of sequences – ignoring the biological significance of sequence differences. A suite of sophisticated likelihood based statistical models from the field of molecular evolution provides the basis for extracting the information from the full distribution of sequence variation. The number of different problems to which phylogeny-based maximum likelihood calculations can be applied is extensive. Available software packages that can perform likelihood calculations suffer from a lack of flexibility and scalability, or employ error-prone approaches to model parameterisation. Results Here we describe the implementation of PyEvolve, a toolkit for the application of existing, and development of new, statistical methods for molecular evolution. We present the object architecture and design schema of PyEvolve, which includes an adaptable multi-level parallelisation schema. The approach for defining new methods is illustrated by implementing a novel dinucleotide model of substitution that includes a parameter for mutation of methylated CpG's, which required 8 lines of standard Python code to define. Benchmarking was performed using either a dinucleotide or codon substitution model applied to an alignment of BRCA1 sequences from 20 mammals, or a 10 species subset. Up to five-fold parallel performance gains over serial were recorded. Compared to leading alternative software, PyEvolve exhibited significantly better real world performance for parameter rich models with a large data set, reducing the time required for optimisation from ~10 days to ~6 hours. Conclusion PyEvolve provides flexible functionality that can be used either for statistical modelling of molecular evolution, or the development of new methods in the field. The toolkit can be used interactively or by writing and executing scripts. The toolkit uses efficient processes for specifying the parameterisation of statistical models, and implements numerous optimisations that make highly parameter rich likelihood functions solvable within hours on multi-cpu hardware. PyEvolve can be readily adapted in response to changing computational demands and hardware configurations to maximise performance. PyEvolve is released under the GPL and can be downloaded from .

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Author and article information

Journal

Journal ID (nlm-ta): Genome Biol Evol

Journal ID (iso-abbrev): Genome Biol Evol

Journal ID (publisher-id): gbe

Title: Genome Biology and Evolution

Publisher: Oxford University Press

ISSN (Electronic): 1759-6653

Publication date Collection: October 2017

Publication date (Electronic): 23 August 2017

Publication date PMC-release: 23 August 2017

Volume: 9

Issue: 10

Pages: 2522-2545

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

Author notes

Associate editor: Dorothée Huchon

Data deposition: This Whole Genome Shotgun sequencing project has been deposited at DDBJ/ENA/GenBank under the accession NIFN00000000. The version described in this article is version NIFN01000000. Specimen Sequoia blood sample deposited as CAS:ORN:98821, California Academy of Sciences, San Francisco, California, United States. Strix occidentalis caurina raw genomic DNA sequences obtained from CAS:ORN:98821 are available from NCBI Sequence Read Archive (SRA) (SRA run accessions SRR4011595, SRR4011596, SRR4011597, SRR4011614, SRR4011615, SRR4011616, SRR4011617, SRR4011618, SRR4011619, and SRR4011620). Strix varia raw genomic DNA sequences obtained from CNHM<USA-OH>:ORNITH:B41533 are available from NCBI SRA (SRA run accessions SRR5428115, SRR5428116, and SRR5428117). Program ScaffSplitN50s deposited at Zenodo http://doi.org/10.5281/zenodo.163683 and available from https://github.com/calacademy-research/ScaffSplitN50s. Program dupchk deposited at Zenodo http://doi.org/10.5281/zenodo.163722 and available from https://github.com/calacademy-research/dupchk. Program GItaxidIsVert deposited at Zenodo http://doi.org/10.5281/zenodo.163737 and available from https://github.com/calacademy-research/GItaxidIsVert. Program scafSeqContigInfo deposited at Zenodo http://doi.org/10.5281/zenodo.163748 and available from https://github.com/calacademy-research/scafSeqContigInfo. Program scafN50 deposited at Zenodo http://doi.org/10.5281/zenodo.163739 and available from https://github.com/calacademy-research/scafN50. Additional scripts deposited as NSO-genome-scripts at Zenodo http://doi.org/10.5281/zenodo.805012 and available from https://github.com/calacademy-research/NSO-genome-scripts. Gene and repeat annotation files, the raw variant call file, alignments of light-associated gene orthologs as well as assemblies of transcriptome sequences deposited at Zenodo http://doi.org/10.5281/zenodo.822859.

[* ]Corresponding author: E-mail: zachanna@ 123456berkeley.edu .

Article

Publisher ID: evx158

DOI: 10.1093/gbe/evx158

PMC ID: 5629816

PubMed ID: 28992302

SO-VID: 1146fce6-8f1f-411b-9b65-d7fdf60ab625

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This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Date accepted : 22 August 2017

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

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Genome Integrity

Most cited references 95

Repbase update: a database and an electronic journal of repetitive elements.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

PyEvolve: a toolkit for statistical modelling of molecular evolution

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