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1.
Figure 4

Figure 4. Cluster of the CfERVs with annotated HERV-Fc-like Pol puteins in relation to reference retroviruses.. From: The First Sequenced Carnivore Genome Shows Complex Host-Endogenous Retrovirus Relationships.

An unrooted NJ tree constructed with a putative evolutionary relationship between HERV-Fc-like CfERV proviruses and their external counterparts. Detected chains are grouped by genus with characteristic colors (green for the gamma-like and yellow for the unclassified). Confidence values to the most deep tree branches are specified over a bootstrapping set of 1000 repetitions. A black asterisk symbolizes a degree of confidence over 90% and solid black circle a higher confidence than 75%.

Álvaro Martínez Barrio, et al. PLoS One. 2011;6(5):e19832.
2.
Figure 2

Figure 2. Gene neighboring CfERVs plot.. From: The First Sequenced Carnivore Genome Shows Complex Host-Endogenous Retrovirus Relationships.

On the x-axis, the distance in bp 3′ and 5′ of the CfERVs in a 200 kb surrounding window [-100 kb, 100 kb] are shown. Position zero refers to the exact location of the CfERV. The presence of genes within each region is shown for the sense (in blue) and antisense (in red) strands. The region with the highest number of genes is marked with the number of genes indicated. A) UCSC RefSeq dog annotated genes; B) including all other UCSC listed species (except dog) annotated genes (xref); C) protein coding genes annotated with only UCSC projections of human genes in the dog genome; D) UCSC xref track annotations counting only ncRNA human genes. E) anciently integrated (>10% LTR divergence); F) intermediately integrated (> = 5% and < = 10%); G) recently integrated (<5%). A visual explanation of the methodology used to calculate the histogram values is sketched in Fig. 3B.

Álvaro Martínez Barrio, et al. PLoS One. 2011;6(5):e19832.
3.
Figure 5

Figure 5. Classification of Fc-like CfERVs with Pol puteins.. From: The First Sequenced Carnivore Genome Shows Complex Host-Endogenous Retrovirus Relationships.

Upper panel left, rooted tree on the fish WDSV shows the relationship between aligned CfERVs and bootstrapped values (n = 1000). Upper panel right: alignment window where horizontal white bars indicate the presence of aligned viral sequence, larger squared ends represent open gaps, and vertical blue colors indicate the degree of similarity (i.e. light: high, dark: low). Lower panel: three different un-rooted phylograms with WDSV to approximate a root point (red square joint) and zoomed views over dense branches of the tree. A) genus-labeled phylogram, gamma-like and unclassified elements in green and yellow respectively. B) Age classification phylogram, youngest elements in light blue, ancient in dark, undated CfERVs in black. C) Score classification phylogram, highest scoring elements in bright red color. A color scale to measure the variation in tone is provided for both B) and C).

Álvaro Martínez Barrio, et al. PLoS One. 2011;6(5):e19832.
4.
Figure 1

Figure 1. From: The First Sequenced Carnivore Genome Shows Complex Host-Endogenous Retrovirus Relationships.

A) Chromosomal distribution of CfERVs. Every CfERV is placed into its chromosomal position rescaled to a megabase (Mb) size bin to be noticeable in the chromosomal picture. A color code is assigned depending on its classified genus. Non-acrocentric chromosomes (chrX) present arrows point at their centromeres. B) Cumulative histogram distinguishing the numbers and genus categories of CfERVs distributed per chromosome. Breaks in bar plots indicate scale changes. C) Cumulative histogram with the CfERV amount of nucleotides contained in exonic, intronic, intergenic or untranslated (UTR) regions per chromosome analyzed. Breaks in bar plots indicate scale changes. D) LINEs (old non-LTR transposable integrations); E) SINE_Cf (newer non-autonomous integrations in dogs). Repeats are grouped in bins to a resolution of 1 Mbp. Relative chromosomal occupancy by these elements of a bin is symbolized by the degree of hue in a grey color scale (darkest, higher). Herein, every CfERV is denoted as specified before. F) Distances to telomeres. The boxplot “Start” describes the distribution of CfERV (or repeat) distances to the telomere at the start of the chromosome, the “End” group is towards the other end of the chromosome. In this graph, the number of elements is represented by ‘n’ (number of chromosomes) and the minimum value in the distribution is ‘min’ for sake of clarity. A number of 0 indicates the fact that an integration of repeat(CfERV) in a telomere exists. Note the different scale in measures (in bp) between images (from left to right): CfERVs contained in each chromosome, LINEs, SINEs-Cf, and repeats without difference of class/type annotated by RepetMasker.

Álvaro Martínez Barrio, et al. PLoS One. 2011;6(5):e19832.
5.
Figure 3

Figure 3. Gene neighborhood statistics.. From: The First Sequenced Carnivore Genome Shows Complex Host-Endogenous Retrovirus Relationships.

A) Histogram based on the gene vicinity graphs of Fig. 2. Plots indicate the total distribution of genes in the antisense and sense strands. The total number of nucleotides from the longest RefSeq transcript composition overlapping within 200kb context relative to the CfERV integrations and their orientations were measured. Where the presence of a greater number of genes on the antisense –relative to CfERV- strand is found, we classify this in the over-represented category, whereas the presence of more genes on the sense strand –relative to CfERV- is classified as under-represented. This is performed for all regions within 100kb on both sides of every CfERV. From left to right: a) UCSC RefSeq dog annotated genes, b) UCSC listed species (except dog) annotated genes, c) genes annotated with only UCSC projections of human genes in the dog genome, d) UCSC xref track annotations counting only ncRNA human genes, e) only recent integrations (<5% LTR divergence) against UCSC xref track annotations, f) intermediately aged CfERVs (> = 5% and < = 10%), and g) ancient CfERVs (>10%). B) Schematic view explaining the methodology employed to calculate the histogram values of Fig. 2. From top to bottom, from a CfERV integrated in sense (U3-RU5-puteins-U3-RU5), we search a 100kb surrounding for transcripts in the same sense of transcriptional direction (light blue) as well as opposite (dark yellow). Another example, with a CfERV integrated in antisense (RU5-U3-puteins-RU5-U3) is also depicted with transcripts in the opposite (dark yellow) and same relative transcriptional direction (light blue). Each set of overlapping transcripts is composed into a common model of transcripts in antisense (red) and in sense (blue) relative to CfERVs. The blue line has been thickened to highlight the places where both curves take equal values. These models are counted into a −100kb to +100kb histogram where the total of CfERVs detected are centered in position 0. A value for this position suggests that any transcript overlaps any part of the CfERVs, as shown in the example. Finally, for the histogram in Fig. 3A, the x-axis is iterated counting the number of positions where the red curve (antisense) takes a higher value than the blue (sense) depicted in dark blue. These positions sum up to the green bars in the histogram in the A panel, being the opposite situation reflected in the green bars where the blue curve (sense) is higher to the red (antisense). When these two curves take the same exact value, the resultant positions are summed in the dark yellow bars.

Álvaro Martínez Barrio, et al. PLoS One. 2011;6(5):e19832.

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