Effects of <i>Tau</i> values on percent false negative and positive calls based on the hybridization results of strain LS411.

<p>Left axis indicates percent false positive (□) and false negative (Δ) Right axis indicates percent reproducibility (○) from the three LS411 hybridization results.</p

Relatedness analysis of the compatible parsimony informative genes from the 38 strains of <i>L. monocytogenes</i>.

<p>The tree was generated from the concatenated gene contents using neighbor joining with the uncorrected <i>p</i> distance. The colors indicated the serotype of <i>L. monocytogenes</i> strains (red; serotype 4b, green; serotype 1/2b and blue; serotype 1/2a). Scale bar represents number of gene differences (present or absent) per gene site.</p

Effects of <i>Tau</i> values on gene present calls (LS402; A, LS406; B and LS411; C) and percent reproducibility (LS402; D, LS406; E and LS411; F).

<p>Effects of <i>Tau</i> values on gene present calls (LS402; A, LS406; B and LS411; C) and percent reproducibility (LS402; D, LS406; E and LS411; F).</p

<i>Listeria monocytogenes</i> genome sequences used in the <i>Listeria</i> GeneChip design.

1<p>The serotype was determined by BLAST analysis of the sequence with the serotype specific primers as reported by Doumith et al, 2004 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032896#pone.0032896-Doumith2" target="_blank">[17]</a></p

Scatter plots of the summarized Robust Multi-array Averaging (RMA) intensities from the triplicate experiments of strains LS402 (A, B), LS406 (C, D), and LS411 (E, F).

<p>Scatter plots of the summarized Robust Multi-array Averaging (RMA) intensities from the triplicate experiments of strains LS402 (A, B), LS406 (C, D), and LS411 (E, F).</p

Comparison of the summarized Robust Multi-array Averaging (RMA) intensities by scatter plots.

<p>Between strains from the same epidemic clones (ECIV) and pathotypes; FG, LS402 and LS406 (A) and Inv; LS415 and LS416 (B). Between strains from the same epidemic clones (ECI) and pathotype (Inv), different outbreaks; LS411 and LS413 (C). Between strains from the same epidemic clones (ECIV), different pathotype; Inv, LS415 and FG, LS406 (D). Red dots indicate summarized RMA intensity differences of less than or equal to 2-fold between two strains. Blue dots indicate RMA intensity differences of more than 2-fold between two strains.</p

Three-dimensional structure analysis of the 11 ORF0 proteins.

<p>All structures are depicted as a cartoon diagram. Within the represented family, the secondary elements are colored in red (α-helix), yellow (β-sheet) and green (coils)</p

The sequence structure of <i>Retrosat2</i> LTR.

<p>The LTR is divided into three regions, U3 (1–244), R (245–2266) and U5 (2267–3292). Red rectangle denotes tandem repeats and black arrows indicate the 10-bp inverted terminal repeats of the LTR.</p

Southern blot of Retrosat2.

<p>(1) Oryza brachyantha, (2) Oryza sativa (Nipponbare), (3) Oryza glaberrima, (4) Oryza nivara, (5) Oryza longistaminata, (6) <i>Oryza rufipogon</i>, (7) <i>Oryza minuta</i>, (8) <i>Oryza officinalis</i>, (9) <i>Oryza punctata</i>, (10) <i>Oryza alta</i>, (11) <i>Oryza australiensis</i>, (12) <i>Oryza granulata</i>, (13) <i>Oryza ridleyi</i>, (14) <i>Oryza coarctata</i> and (15) <i>Oryza brachyantha</i>.</p

Functional and Structural Divergence of an Unusual LTR Retrotransposon Family in Plants

<div><p>Retrotransposons with long terminal repeats (LTRs) more than 3 kb are not frequent in most eukaryotic genomes. Rice LTR retrotransposon, <em>Retrosat2</em>, has LTRs greater than 3.2 kb and two open reading frames (ORF): ORF1 encodes enzymes for retrotransposition whereas no function can be assigned to ORF0 as it is not found in any other organism. A variety of experimental and <em>in silico</em> approaches were used to determine the origin of <em>Retrosat2</em> and putative function of ORF0. Our data show that not only is <em>Retrosat2</em> highly abundant in the <em>Oryza</em> genus, it may yet be active in rice. Homologs of <em>Retrosat2</em> were identified in maize, sorghum, Arabidopsis and other plant genomes suggesting that the <em>Retrosat2</em> family is of ancient origin. Several putatively cis-acting elements, some multicopy, that regulate retrotransposon replication or responsiveness to environmental factors were found in the LTRs of <em>Retrosat2</em>. Unlike the ORF1, the ORF0 sequences from <em>Retrosat2</em> and homologs are divergent at the sequence level, 3D-structures and predicted biological functions. In contrast to other retrotransposon families, <em>Retrosat2</em> and its homologs are dispersed throughout genomes and not concentrated in the specific chromosomal regions, such as centromeres. The genomic distribution of <em>Retrosat2</em> homologs varies across species which likely reflects the differing evolutionary trajectories of this retrotransposon family across diverse species.</p> </div