<strong>StrOccCau_1.0_nuc_masked.fa.bz2</strong> : This FASTA format file compressed ... more <strong>StrOccCau_1.0_nuc_masked.fa.bz2</strong> : This FASTA format file compressed with bzip2 is the file that you will most likely want to download if you would like to perform an alignment to this genome assembly. This file is the repeat-masked assembly output from SOAPdenovo2 toolkit GapCloser version 1.12-r6 (Luo et al. 2012) without any contigs and scaffolds less than 1,000 nt and also without the contigs and scaffolds that we identified either as the mitochondrial genome sequence or as contaminant sequences. <strong>StrOccCau_1.0_nuc.fa.bz2</strong> : This FASTA format file compressed with bzip2 is the file that we uploaded to the NCBI Whole Genome Shotgun (WGS) project database. This file is the assembly output from SOAPdenovo2 toolkit GapCloser version 1.12-r6 (Luo et al. 2012) without any contigs and scaffolds less than 1,000 nt and also without the contigs and scaffolds that we identified either as the mitochondrial genome sequence or as contaminant sequences. <strong>StrOccCau_1.0_mito.fa</strong> : This FASTA format file is the mitochondrial-genome-derived scaffold from the assembly output from SOAPdenovo2 toolkit GapCloser version 1.12-r6 (Luo et al. 2012). <strong>StrOccCau_1.0.gff.bz2</strong> : This gff format file compressed this file with bzip2 contains the gene annotations of StrOccCau_1.0_nuc.fa. <strong>StrOccCau_1.0_transcripts.fa.bz2</strong> : This FASTA format file compressed this file with bzip2 contains the sequences of the gene transcript sequences of the genes annotated in StrOccCau_1.0.gff. <strong>StrOccCau_1.0_proteins.fa.bz2</strong> : This FASTA format file compressed this file with bzip2 contains the protein sequences of the genes annotated in StrOccCau_1.0.gff. <strong>StrOccCau_1.0_RM_homology_includes_LowComplexity.out.bz2</strong> : This file provides the repeat annotations produced by the homology-based masking of StrOccCau_1.0_nuc.fa that included masking of low complexity regions and simple repeats. We compressed this file with bzip2. <strong>StrOccCau_1.0_RM_DeN [...]
Many poisonous organisms carry small-molecule toxins that alter voltage-gated sodium channel (NaV... more Many poisonous organisms carry small-molecule toxins that alter voltage-gated sodium channel (NaV) function. Among these, batrachotoxin (BTX) from Pitohui poison birds and Phyllobates poison frogs stands out because of its lethality and unusual effects on NaV function. How these toxin-bearing organisms avoid autointoxication remains poorly understood. In poison frogs, a NaV DIVS6 pore-forming helix N-to-T mutation has been proposed as the BTX resistance mechanism. Here, we show that this variant is absent from Pitohui and poison frog NaVs, incurs a strong cost compromising channel function, and fails to produce BTX-resistant channels in poison frog NaVs. We also show that captivity-raised poison frogs are resistant to two NaV-directed toxins, BTX and saxitoxin (STX), even though they bear NaVs sensitive to both. Moreover, we demonstrate that the amphibian STX “toxin sponge” protein saxiphilin is able to protect and rescue NaVs from block by STX. Taken together, our data contradict t...
We analyzed whole-genome data of four spotted owls (Strix occidentalis) to provide a broad-scale ... more We analyzed whole-genome data of four spotted owls (Strix occidentalis) to provide a broad-scale assessment of the genome-wide nucleotide diversity acrossS. occidentalispopulations in California. We assumed that each of the four samples was representative of its population and we estimated effective population sizes through time for each corresponding population. Our estimates provided evidence of long-term population declines in all CaliforniaS. occidentalispopulations. We found no evidence of genetic differentiation between northern spotted owl (S. o. caurina) populations in the counties of Marin and Humboldt in California. We estimated greater differentiation between populations at the northern and southern extremes of the range of the California spotted owl (S. o. occidentalis) than between populations ofS. o. occidentalisandS. o. caurinain northern California. The San Diego CountyS. o. occidentalispopulation was substantially diverged from the other threeS. occidentalispopulati...
<strong>StrOccCau_1.0_nuc_masked.fa.bz2</strong> : This FASTA format file compressed ... more <strong>StrOccCau_1.0_nuc_masked.fa.bz2</strong> : This FASTA format file compressed with bzip2 is the file that you will most likely want to download if you would like to perform an alignment to this genome assembly. This file is the repeat-masked assembly output from SOAPdenovo2 toolkit GapCloser version 1.12-r6 (Luo et al. 2012) without any contigs and scaffolds less than 1,000 nt and also without the contigs and scaffolds that we identified either as the mitochondrial genome sequence or as contaminant sequences. <strong>StrOccCau_1.0_nuc.fa.bz2</strong> : This FASTA format file compressed with bzip2 is the file that we uploaded to the NCBI Whole Genome Shotgun (WGS) project database. This file is the assembly output from SOAPdenovo2 toolkit GapCloser version 1.12-r6 (Luo et al. 2012) without any contigs and scaffolds less than 1,000 nt and also without the contigs and scaffolds that we identified either as the mitochondrial genome sequence or as contaminant sequences. <strong>StrOccCau_1.0_mito.fa</strong> : This FASTA format file is the mitochondrial-genome-derived scaffold from the assembly output from SOAPdenovo2 toolkit GapCloser version 1.12-r6 (Luo et al. 2012). <strong>StrOccCau_1.0.gff.bz2</strong> : This gff format file compressed this file with bzip2 contains the gene annotations of StrOccCau_1.0_nuc.fa. <strong>StrOccCau_1.0_transcripts.fa.bz2</strong> : This FASTA format file compressed this file with bzip2 contains the sequences of the gene transcript sequences of the genes annotated in StrOccCau_1.0.gff. <strong>StrOccCau_1.0_proteins.fa.bz2</strong> : This FASTA format file compressed this file with bzip2 contains the protein sequences of the genes annotated in StrOccCau_1.0.gff. <strong>StrOccCau_1.0_RM_homology_includes_LowComplexity.out.bz2</strong> : This file provides the repeat annotations produced by the homology-based masking of StrOccCau_1.0_nuc.fa that included masking of low complexity regions and simple repeats. We compressed this file with bzip2. <strong>StrOccCau_1.0_RM_DeN [...]
Many poisonous organisms carry small-molecule toxins that alter voltage-gated sodium channel (NaV... more Many poisonous organisms carry small-molecule toxins that alter voltage-gated sodium channel (NaV) function. Among these, batrachotoxin (BTX) from Pitohui poison birds and Phyllobates poison frogs stands out because of its lethality and unusual effects on NaV function. How these toxin-bearing organisms avoid autointoxication remains poorly understood. In poison frogs, a NaV DIVS6 pore-forming helix N-to-T mutation has been proposed as the BTX resistance mechanism. Here, we show that this variant is absent from Pitohui and poison frog NaVs, incurs a strong cost compromising channel function, and fails to produce BTX-resistant channels in poison frog NaVs. We also show that captivity-raised poison frogs are resistant to two NaV-directed toxins, BTX and saxitoxin (STX), even though they bear NaVs sensitive to both. Moreover, we demonstrate that the amphibian STX “toxin sponge” protein saxiphilin is able to protect and rescue NaVs from block by STX. Taken together, our data contradict t...
We analyzed whole-genome data of four spotted owls (Strix occidentalis) to provide a broad-scale ... more We analyzed whole-genome data of four spotted owls (Strix occidentalis) to provide a broad-scale assessment of the genome-wide nucleotide diversity acrossS. occidentalispopulations in California. We assumed that each of the four samples was representative of its population and we estimated effective population sizes through time for each corresponding population. Our estimates provided evidence of long-term population declines in all CaliforniaS. occidentalispopulations. We found no evidence of genetic differentiation between northern spotted owl (S. o. caurina) populations in the counties of Marin and Humboldt in California. We estimated greater differentiation between populations at the northern and southern extremes of the range of the California spotted owl (S. o. occidentalis) than between populations ofS. o. occidentalisandS. o. caurinain northern California. The San Diego CountyS. o. occidentalispopulation was substantially diverged from the other threeS. occidentalispopulati...
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