Sequence comparison of prefrontal cortical brain transcriptome from a tame and an aggressive silver fox (Vulpes vulpes)

<p>Abstract</p> <p>Background</p> <p>Two strains of the silver fox (<it>Vulpes vulpes</it>), with markedly different behavioral phenotypes, have been developed by long-term selection for behavior. Foxes from the tame strain exhibit friendly behavior towards humans, paralleling the sociability of canine puppies, whereas foxes from the aggressive strain are defensive and exhibit aggression to humans. To understand the genetic differences underlying these behavioral phenotypes fox-specific genomic resources are needed.</p> <p>Results</p> <p>cDNA from mRNA from pre-frontal cortex of a tame and an aggressive fox was sequenced using the Roche 454 FLX Titanium platform (> 2.5 million reads & 0.9 Gbase of tame fox sequence; >3.3 million reads & 1.2 Gbase of aggressive fox sequence). Over 80% of the fox reads were assembled into contigs. Mapping fox reads against the fox transcriptome assembly and the dog genome identified over 30,000 high confidence fox-specific SNPs. Fox transcripts for approximately 14,000 genes were identified using SwissProt and the dog RefSeq databases. An at least 2-fold expression difference between the two samples (p < 0.05) was observed for 335 genes, fewer than 3% of the total number of genes identified in the fox transcriptome.</p> <p>Conclusions</p> <p>Transcriptome sequencing significantly expanded genomic resources available for the fox, a species without a sequenced genome. In a very cost efficient manner this yielded a large number of fox-specific SNP markers for genetic studies and provided significant insights into the gene expression profile of the fox pre-frontal cortex; expression differences between the two fox samples; and a catalogue of potentially important gene-specific sequence variants. This result demonstrates the utility of this approach for developing genomic resources in species with limited genomic information.</p

Fourier Transform Infrared (FTIR) Spectroscopic Analyses of Microbiological Samples and Biogenic Selenium Nanoparticles of Microbial Origin: Sample Preparation Effects

To demonstrate the importance of sample preparation used in Fourier transform infrared (FTIR) spectroscopy of microbiological materials, bacterial biomass samples with and without grinding and after different drying periods (1.5–23 h at 45 °C), as well as biogenic selenium nanoparticles (SeNPs; without washing and after one to three washing steps) were comparatively studied by transmission FTIR spectroscopy. For preparing bacterial biomass samples, Azospirillum brasilense Sp7 and A. baldaniorum Sp245 (earlier known as A. brasilense Sp245) were used. The SeNPs were obtained using A. brasilense Sp7 incubated with selenite. Grinding of the biomass samples was shown to result in slight downshifting of the bands related to cellular poly-3-hydroxybutyrate (PHB) present in the samples in small amounts (under ~10%), reflecting its partial crystallisation. Drying for 23 h was shown to give more reproducible FTIR spectra of bacterial samples. SeNPs were shown to contain capping layers of proteins, polysaccharides and lipids. The as-prepared SeNPs contained significant amounts of carboxylated components in their bioorganic capping, which appeared to be weakly bound and were largely removed after washing. Spectroscopic characteristics and changes induced by various sample preparation steps are discussed with regard to optimising sample treatment procedures for FTIR spectroscopic analyses of microbiological specimens

Anterior Pituitary Transcriptome Suggests Differences in ACTH Release in Tame and Aggressive Foxes

Domesticated species exhibit a suite of behavioral, endocrinological, and morphological changes referred to as “domestication syndrome.” These changes may include a reduction in reactivity of the hypothalamic-pituitary-adrenal (HPA) axis and specifically reduced adrenocorticotropic hormone release from the anterior pituitary. To investigate the biological mechanisms targeted during domestication, we investigated gene expression in the pituitaries of experimentally domesticated foxes (Vulpes vulpes). RNA was sequenced from the anterior pituitary of six foxes selectively bred for tameness (“tame foxes”) and six foxes selectively bred for aggression (“aggressive foxes”). Expression, splicing, and network differences identified between the two lines indicated the importance of genes related to regulation of exocytosis, specifically mediated by cAMP, organization of pseudopodia, and cell motility. These findings provide new insights into biological mechanisms that may have been targeted when these lines of foxes were selected for behavior and suggest new directions for research into HPA axis regulation and the biological underpinnings of domestication

Genes located inside or within 50,000 bp from start and end of the multi SNP clusters in the dog genome.

<p>Cluster numbers refer to the numbering from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127013#pone.0127013.t002" target="_blank">Table 2</a>.</p><p>Genes located inside or within 50,000 bp from start and end of the multi SNP clusters in the dog genome.</p

SNP minor allele frequency and heterozygosity in tame and aggressive populations.

<p>SNP minor allele frequency and heterozygosity in tame and aggressive populations.</p

Principal component analysis.

<p>Principal component analysis of SNP data for 20 tame and 20 aggressive foxes. 8,437 SNPs with genotypes available for all individuals were used in this analysis. Aggressive individuals are represented by red dots, tame individuals are represented by green triangles. PC1 is plotted on the x-axis, PC2 is plotted on the y-axis.</p

Estimation of linkage disequilibrium (r²) in tame and aggressive fox populations.

<p>Distributions of r^<b>2</b> values between pairs of SNPs separated by different distances are compared between tame (green) and aggressive (red) populations. SNP pairs were divided into 14 sets (bins) using the estimated distances between SNPs in the fox genome (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127013#pone.0127013.s007" target="_blank">S2 Table</a>). Each bin is represented by a doubled bar (green and red) on the graph. The range of distances between SNPs in each bin is indicated on the x-axis. The width of the bar represents the relative number of SNP pairs in that bin for that population after a log transformation (wider bars have more pairs of SNPs). Exact numbers of SNP pairs in each bin are presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127013#pone.0127013.s007" target="_blank">S2 Table</a>. The y-axis indicates r^<b>2</b> values for pairs of SNPs. The yellow diamonds correspond to the mean r^<b>2</b> for all SNPs in that bin in the population. The white circles correspond to the median values. The thin black line within each bar represents r^<b>2</b> values in that bin in the population in the interval from the 25th to 75th percentile. The horizontal line corresponds r^<b>2</b> = 0.2.</p

Estimation of population structure using STRUCTURE.

<p>Cluster analysis of fox genotypes was performed at four values of K (2, 3, 4, and 5) without population information. The numbers of assumed clusters are indicated on the y-axis. The population origin of individuals is indicated on x-axis. On each graph the individuals are listed in the order obtained at K = 3. Each individual is represented by a bar that is segmented into colors based on the assignment into inferred clusters given the assumption of K populations. The length of the colored segment is the estimated proportion of the individual’s genome belonging to that cluster. The analysis was run in 8 replicates for each K, the replicate with the highest likelihood is shown. The genetic structure analysis clearly differentiated the tame population from the aggressive one and did not reveal significant population stratification within the tame population at every K tested. In contrast, the population stratification within the aggressive population became apparent at K = 3.</p