Number of gross rearrangement events for each <i>Drosophila</i> species.

<p>Interrupting sequence, deletions, inversions and duplications affecting at least 200 bases of numt sequence in the nuclear genomes after insertion are shown. The number of distinct numts affected is shown in parentheses. Multiple rearrangements of the same type were only counted once for each numt.</p

Mitochondrial origins of numts.

<p>Locations of origin of numt sequences (black) in the mitochondrial genomes (grey) for 11 <i>Drosophila</i> species are shown. The <i>D. melanogaster</i> mitochondrial assembly is relatively large, because it has a larger portion of the variable control region sequenced.</p

Age of numt insertions.

<p>Average frequencies (insertions per million years) of numt insertions on each branch of the <i>Drosophila</i> tree are shown. In parentheses is the number of extant numts that have arisen by duplication (left), and the number of distinct paralog sets (right). Divergence times were derived from TimeTree <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032593#pone.0032593-Hedges1" target="_blank">[47]</a> and the tree toplogy from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032593#pone.0032593-Clark1" target="_blank">[20]</a>.</p

Insertion and duplication rates for each lineage.

<p>Duplication rates were calculated both including and excluding multiple duplications from the same paralog set, and using only terminal branches of the tree. No duplications were observed in <i>D. melanogaster</i> and <i>D. simulans</i>.</p

Numbers of numt annotations in 11 <i>Drosophila</i> species.

*<p>Genome size estimated by assembly size <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032593#pone.0032593-Clark1" target="_blank">[20]</a>.</p>**<p>Repeat content annotated by ReAS <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032593#pone.0032593-Li3" target="_blank">[48]</a>, excluding scaffolds <200 kb <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032593#pone.0032593-Clark1" target="_blank">[20]</a>.</p>***<p>Average numt length excludes internal duplications and interrupting sequence between merged fragments.</p

Additional file 2: of Abundant expression of somatic transposon-derived piRNAs throughout Tribolium castaneum embryogenesis

Orientation of RepeatMasker annotations within piRNA clusters. Left: the strand-bias of the top 50 most piRNA-enriched clusters of the T. castaneum genome. Right: the number of regions identified as homologous to known TEs by RepeatMasker on the positive (red) and negative (blue) DNA strands per piRNA cluster. (PDF 391 kb

qPCR verification of expression of selected sense/antisense pairs.

<p>Expression of both the sense and antisense transcript for NCU04182, NCU07268, NCU02607, NCU07915, NCU09135 and NCU09136 in the WT is shown, after growth in the dark, and exposure to light and temperature pulses. Black bars indicate the protein-coding sense transcript and white bars indicate its antisense transcript. Error bars represent standard deviation. Statistical significance between light vs dark and temperature vs dark was determined using Student t test, * indicates <i>p</i>-value <0.05 and ** indicates <i>p</i>-value < = 0.005. n = 3.</p

Genomic distribution of annotated and lncRNA transcripts.

<p>Annotated genes from the BROAD database are depicted in blue and those that are expressed above a threshold of > = 50 reads in our combined datasets are depicted in black. The distribution of all lncRNAs is shown in green and antisense transcripts are shown in red. Large gaps in the gene annotation indicate centromeric regions.</p

List of lncRNAs differentially expressed in response to light.

<p>*Locus information can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091353#pone.0091353.s004" target="_blank">Table S2</a>.</p

Examples of sense/antisense transcript pairs annotated from RNA sequencing data and validated by qPCR.

<p>Panels display the locations and distribution of RNAseq reads of sense protein-coding (black) and antisense lncRNA (pink) transcripts. RNAseq reads from the WT dark (D), light pulse (L) and temperature pulse (T) samples mapping to each locus are shown; read count scales differ. Below each panel, arrows represent sense (black) and antisense (pink) transcripts. Thick lines represent exons and thin lines introns. Grey boxes indicate the approximate region of each transcript amplified by qRTPCR. Reads are shown for the following sense transcripts and their complementary antisense RNAs: NCU04182 (coding for splicing factor 3 b subunit 4), NCU07268 (coding for a hypothetical protein with PAS domain), NCU02607 (coding for hypothetical protein), NCU07915 (coding for integral membrane protein), NCU09135 (coding for phosphatidylinositol phospholipase C) and NCU09136 (coding for a hypothetical protein. A single antisense transcript overlaps both NCU09135 and NCU09136. The two transcripts antisense to NCU09136 are separated by more than 200 nts.</p