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

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

A New Threat to Honey Bees, the Parasitic Phorid Fly Apocephalus borealis

Honey bee colonies are subject to numerous pathogens and parasites. Interaction among multiple pathogens and parasites is the proposed cause for Colony Collapse Disorder (CCD), a syndrome characterized by worker bees abandoning their hive. Here we provide the first documentation that the phorid fly Apocephalus borealis, previously known to parasitize bumble bees, also infects and eventually kills honey bees and may pose an emerging threat to North American apiculture. Parasitized honey bees show hive abandonment behavior, leaving their hives at night and dying shortly thereafter. On average, seven days later up to 13 phorid larvae emerge from each dead bee and pupate away from the bee. Using DNA barcoding, we confirmed that phorids that emerged from honey bees and bumble bees were the same species. Microarray analyses of honey bees from infected hives revealed that these bees are often infected with deformed wing virus and Nosema ceranae. Larvae and adult phorids also tested positive for these pathogens, implicating the fly as a potential vector or reservoir of these honey bee pathogens. Phorid parasitism may affect hive viability since 77% of sites sampled in the San Francisco Bay Area were infected by the fly and microarray analyses detected phorids in commercial hives in South Dakota and California's Central Valley. Understanding details of phorid infection may shed light on similar hive abandonment behaviors seen in CCD

Images of <i>Apocephalus borealis</i> and honey bees.

<p>(A) Adult female <i>A. borealis</i>. (B) Female <i>A. borealis</i> ovipositing into the abdomen of a worker honey bee. (C) Two final instar larvae of <i>A. borealis</i> exiting a honey bee worker at the junction of the head and thorax (red arrows).</p

Gene annotations for <i>Strix occidentalis caurina</i> draft nuclear genome assembly version 1

NSO-wgs-v1-nuc.gff.bz : This file provides the gene annotations produced by the MAKER pipeline for the Strix occidentalis caurina draft whole nuclear genome assembly, NSO-wgs-v1-nuc. NSO-wgs-v1-nuc-masked-homology-includes-LowComplexity.out.bz : This file provides the repeat annotations produced by the homology-based masking of NSO-wgs-v1-nuc that included masking of low complexity regions and simple repeats. NSO-wgs-v1-nuc-masked-DeNovo-includes-LowComplexity.out : This file provides the repeat annotations produced by the de novo masking of NSO-wgs-v1-nuc that included masking of low complexity regions and simple repeats. NSO-wgs-v1-nuc-masked-homology-no-LowComplexity.out.bz : This file provides the repeat annotations produced by the homology-based masking of NSO-wgs-v1-nuc that did not include masking of low complexity regions and simple repeats. NSO-wgs-v1-nuc-masked-DeNovo-no-LowComplexity.out : This file provides the repeat annotations produced by the de novo masking of NSO-wgs-v1-nuc that did not include masking of low complexity regions and simple repeats

Distribution of phorid-infected honey bees sampled in this study (red).

<p>Inset shows the San Francisco Bay Area counties where we found phorid-parasitized honey bees. The routes of commercial hives tested are indicated (arrows), where dotted lines represent states the hives crossed before viral microarray testing and solid lines represent the route of hives during the period of microarray testing. Sites where <i>A. borealis</i> was previously known <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029639#pone.0029639-Genersch1" target="_blank">[7]</a> are indicated by black dots.</p

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

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 × 106nt. 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

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

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 × 106nt. 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