Density of chimpanzee-specific ERV copies in chimpanzee chromosomes.

<p>Each bar indicates the density of chimpanzee-specific ERV copies (number of insertion/Mbp of sequences) on each chimpanzee chromosome. The distribution bar is composed of four different colors, each of which represents one of four different PtERV categories: full-length chimpanzee-specific ERV, chimpanzee-specific solitary LTR, truncated PtERV, and unknown types of PtERV. Yellow stars indicate the presence of potential rcPtERVs in the respective chromosome.</p

Summary of chimpanzee-specific ERV loci.

<p>Summary of chimpanzee-specific ERV loci.</p

Polymorphic rcPtERVs in chimpanzee individuals.

<p>Two of eight potential rcPtERV loci were polymorphic and the PCR results are shown in this figure. In the strategy for PCR amplification, the colored arrows indicate the positions of PCR primers; the red and blue arrows indicate forward and reverse flanking primers, respectively. Green and yellow arrows indicate reverse and forward internal primers which are specific to PtERV elements. PCR band in the upper gel picture indicates the absence of the rcPtERV while PCR band in the middle and bottom gel picture indicates the presence of the rcPtERV.</p

Phylogenetic relationship of different retroviral genera.

<p>Maximum-likelihood (ML) dendrograms (1000 bootstraps consensus) of five primate specific-retroviral genera (beta-, gamma-, delta-, lenti-, and spuma-like retrovirus), which are constructed based on the sequences of their Pol reverse transcriptase (RT) and integrase (IN). Chimpanzee-specific ERV copies and HERV-Ks are written in red and blue, respectively. The black scale bar denotes a genetic distance of 0.1 amino acid substitutions per position.</p

Alternative <i>PNRC2</i> transcripts caused by a chimpanzee-specific ERV.

<p>(A) Using the UCSC Genome Browser, the <i>PNRC2</i> gene is anatomized into intron, un-translated region (UTR), and coding exon. (B) The structures of chimpanzee and non-chimpanzee primate <i>PNRC2</i>s and their transcripts are depicted. The black and gray boxes indicate an exon and UTRs, respectively, and the red box denotes the untranscribed UTR1 of the chimpanzee <i>PNRC2</i>. Four different primers used to amplify PCR products are shown in red, blue, green, and black arrows, respectively. The target site duplications (TSDs) of the full-length chimpanzee-specific ERV are written in red. (C) The picture shows an agarose gel image of PCR products. Genomic DNAs from four different primates (human, chimpanzee, gorilla, and orangutan) were used as a DNA template for each PCR reaction.</p

Structural analysis of potential rcPtERVs.

<p>Using the RetroTector 10 program, the eight potential rcPtERVs were fragmented into four parts: <i>gag</i> (internal structural proteins, motifs named CA and NC), <i>pro</i> (protease, motifs named PR), <i>pol</i> (<i>pol</i> gene, motifs named RT, RH and IN), and <i>env</i> (envelope gene, motifs named SU and TM). Each colored box indicates one of the four parts: <i>gag</i> (red), <i>pro</i> (blue), <i>pol</i> (green), and <i>env</i> (orange). The features of the full-length chimpanzee-specific ERV insertions are described in the bottom of the figure.</p

Structure of chimpanzee-specific ERVs.

<p>This figure depicts the structure of six different chimpanzee-specific ERV subfamilies, deposited in the CENSOR database. Each colored box indicates a gene; the red, blue, green, and orange boxes indicate <i>gag</i>, <i>pro</i>, <i>pol</i>, and <i>env</i> gene, respectively. The grey box indicates LTR sequence.</p

Age estimate of PtERV subfamilies.

a<p>The age is calibrated by 0.26% <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101195#pone.0101195-Lavrentieva1" target="_blank">[48]</a> and 0.20% <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101195#pone.0101195-Anderssen1" target="_blank">[49]</a> per site per myr (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101195#s4" target="_blank">Methods</a>).</p

The phylogenetic tree of human-specific HERV-K LTRs.

<p>This is a maximum likelihood tree reconstructed using Kimura-2-parameter distance model. Most HERV-K elements contain an LTR at their 5′ and 3′ ends. In cases where the two LTR sequences are similar to one another, they are shown in the same colour. LTRs from the same element but having divergent sequences are not clustered in the same colour. Short LTRs causing ambiguity on this tree were excluded from this analysis. Bootstrap values for nodes (% of 1000 replicates) scoring higher than 50% are reported.</p

Comparison of human-specific HERV-K108 and HERV-K124 elements.

<p>Both of HERV-K108 and HERV-K124 have two HERV-K internal regions (green). However, their sequence architecture is the result of different mechanisms. (A) HERV-K108. After the insertion of the HERV-K element, non-allelic homologous recombination between two different LTRs (yellow chevrons) of the HERV-K element occurred. This resulted in a locus containing two HERV-K internal regions and three LTRs. This locus retains the original TSDs (red chevrons) created upon its initial insertion. (B) HERV-K124. Compared to the HERV-K108, which has two intact internal regions and three intact LTRs, the second internal region of HERV-K124 has largely deleted and its internal and 3′ LTRs inverted and partially deleted. The mechanism(s) responsible for this element’s sequence architecture is not clearly resolved, but we depict here a potential mechanism capable of generating this element. Yellow boxes indicate standard LTRs, pink boxes indicate inverted partial LTRs, and green boxes indicate HERV-K internal regions.</p