PbTRIM elements preferentially insert into AT-rich region in the <i>P. barbatus</i> genome.

<p>TSDs along with the flanking sequences from 59 complete PbTRIM elements and 112 solo-LTRs were used to generate the sequence logo.</p

Association of PbTRIM with genes in the <i>P. barbatus</i> genome.

<p>Among a total of 243 complete elements, solo-LTRs and element fragments of PbTRIM family, 100 (38%) have overlap with gene exons and/or introns, or located within 1-kb from a predicted gene.</p

Phylogenetic relationships of homologous PbTRIM sequences and their host species.

<p>(A) Neighbor-joining phylogenetic tree of homologous PbTRIM sequences derived from different ant species/lineages. The tree was produced from 36 PbTRIM elements (all belong to subfamily I) originally identified from the <i>P. barbatus</i> genome and 31 partial sequences identified from different ant species/lineages through PCR amplification. Branch lengths are proportional to the genetic distances. Only bootstrap values greater than 50 are shown. Homologous sequences derived from non-<i>Pogonomyrmes</i> ant species/lineages were indicated by different colored shapes. Numbers in brackets denote the clone numbers of individual sequences. Close square brackets indicate elements from different ant species that share high sequence similarity (see text for more details). (B) Phylogenetic relationship of 12 ant genera examined in this study. The tree was generated following Moreau <i>et al.</i> (2006) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053401#pone.0053401-Zhu1" target="_blank">[41]</a> and Brady (2006) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053401#pone.0053401-Tamura1" target="_blank">[47]</a>, with <i>Apis</i> included as an out-group. PbTRIM homologues were found in three of the genera (shown in red) through PCR analysis.</p

A Novel Family of Terminal-Repeat Retrotransposon in Miniature (TRIM) in the Genome of the Red Harvester Ant, <i>Pogonomyrmex barbatus</i>

<div><p>We report the first described non-plant family of TRIMs (terminal-repeat retrotransposons in miniature), which are small nonautonomous LTR retrotransposons, from the whole-genome sequence of the red harvester ant, <i>Pogonomyrmex barbatus</i> (Hymenoptera: Myrmicinae). Members of this retrotransposon family, named PbTRIM, have typical features of plant TRIMs in length and structure, although they share no overall sequence similarity. PbTRIM elements and their solo-LTRs are abundant in the host genome and exhibit an uneven distribution pattern. Elements are preferentially inserted into TA-rich regions with ATAT as the most common pattern of target site duplication (TSD). PbTRIM is most likely mobile as indicated by the young age of many complete elements, the high degree of sequence similarity among elements at different genomic locations, the abundance of elements in the host genome, and the presence of 4-bp target site duplications (TSDs) flanking the elements and solo-LTRs. Many PbTRIM elements and their solo-LTRs are located within or near genes, suggesting their potential roles in restructuring the host genes and genome. Database search, PCR and sequencing analysis revealed the presence of homologous PbTRIM elements in other ant species. The high sequence similarity between elements from distantly related ant species, the incongruence between the phylogenies of PbTRIM and its hosts, and the patchy distribution of the retroelement within the Myrmicinae subfamily indicate possible horizontal transfer events of the retroelement.</p></div

Uneven distribution of PbTRIM elements and their solo-LTRs in the <i>P. barbatus</i> genome.

<p>PbTRIM elements and solo-LTRs tend to form closely located clusters in some genomic regions.</p

Ant species/lineages used for PCR amplification of PbTRIM elements.

<p>Ant species/lineages used for PCR amplification of PbTRIM elements.</p

Nucleotide frequencies of TSD and its flanking sequences of complete elements (n = 59) and solo-LTRs (n = 112) of PbTRIM family.

<p>Nucleotide frequencies of TSD and its flanking sequences of complete elements (n = 59) and solo-LTRs (n = 112) of PbTRIM family.</p

Frequency distribution of the estimated age of 67 complete PbTRIM elements from the <i>P. barbatus</i> genome.

<p>Frequency distribution of the estimated age of 67 complete PbTRIM elements from the <i>P. barbatus</i> genome.</p

Examples of PbTRIM elements and solo-LTRs located within or near genes.

<p>Exons of predicted genes are shown as red boxes, with the last exons denoted as pentagons to indicate the transcription orientation. The solid and the dashed lines represent gene introns and intergenic regions, respectively. The direction of the LTR sequences is indicated by the grey triangles in the open square, and the TSD sequences are shown on the either side of the element or solo-LTR. (A) A complete PbTRIM element is located within 1-kb from the transcription start sites of two genes (upstream: protein SERAC1, downstream: GTP-binding protein ypt7). (B) A complete element contributes sequence to the second exon-intron boundary of the gene encoding SET and MYND domain-containing protein 4. (C) A solo-LTR is located within the first intron of a gene encoding the focal adhesion kinase 1.</p

Phylogenetic relationship among the complete PbTRIM elements identified from the <i>P. barbatus</i> genome.

<p>The neighbor-joining tree was produced with Mega 5.0. The evolutionary distances were computed using the Tamura-Nei method. All branch lengths are drawn to scale. The 64 complete elements included in the analysis can be largely grouped into 4 subfamilies.</p