Hox complex miRNAs and their targets.

<p>(<b>A</b>) Cartoon of <i>Drosophila</i> Hox complex showing locations of miRNA hairpins. Unlabeled genes (pink boxes) are the 3 diverged Hox3 orthologs in <i>Drosophila zen</i>, <i>zen2</i>, and <i>bicoid</i>. // indicates a break in the Hox complex in <i>Drosophila melanogaster</i>. Transcription is generally from right to left. (<b>B</b>) Schematic of <i>mir-10</i> primary transcript and alignment of hairpin sequences from selected bilaterians. Boxed regions indicate miR-10-5p (red) and miR-10-3p (green) sequences. Shading indicates sequences highly conserved with <i>Drosophila</i>. (<b>C</b>) Schematic of <i>mir-iab-4</i> primary transcript and alignment of hairpin sequences from selected arthropods. Boxed regions indicate miR-iab-4-5p (red) and miR-iab-4-3p (green) sequences. Shading indicates sequences highly conserved with <i>Drosophila</i>. (<b>D</b>) Putative duplexes between miR-10-5p and 3′UTR sequences of <i>Scr</i> orthologs in selected arthropods. (<b>E</b>) Putative duplexes between miR-10-3p and 3′UTR sequences of <i>Abd-B</i> orthologs in selected insects. (<b>F</b>) Putative duplexes between miR-iab-4-5p and 3′UTR sequences of <i>Antp</i> orthologs in selected insects. The species shown in (D–F) were chosen to exhibit the ranges of miRNA:target site structures. More potential target sites for these miRNAs in different species are shown aligned in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031365#pone.0031365.s005" target="_blank">Figures S5</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031365#pone.0031365.s006" target="_blank">S6</a>, and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031365#pone.0031365.s009" target="_blank">S9</a>. Colored nucleotides in (D–F) indicate G:U base parings. <i>A.aeg</i> - <i>Aedes aegypti</i>, <i>A.gam</i> - <i>Anopheles gambiae</i>, <i>A.mel</i> - <i>Apis mellifera</i>, <i>A.pis</i> - <i>Acyrthosiphum pisum</i>, <i>B.flo</i> - <i>Branchiostoma floridae</i>, <i>B.mor</i> - <i>Bombyx mori</i>, <i>C.pip</i> - <i>Culex pipiens quinquefasciatus</i>, <i>D.gri</i> - <i>Drosophila grimshawi</i>, <i>D.mel</i> - <i>Drosophila melanogaster</i>, <i>D.pul</i> - <i>Daphnia pulex</i>, <i>D.rer</i> - <i>Danio rerio</i>, <i>D.vir</i> - <i>Drosophila virilus</i>, <i>H.sap</i> - <i>Homo sapiens</i>, <i>I.sca</i> - <i>Ixodes scapularis, L.gig</i> - <i>Lottia gigantea</i>, <i>L.lon</i> - <i>Lutzomyia longipalpis</i>, <i>M.dom</i> - <i>Monodelphis domestica</i>, <i>N.vit</i> - <i>Nasonia vitripennis</i>, <i>P.hum</i> - <i>Pediculus Humanus</i>, <i>R.pro</i> - <i>Rhodnius prolixus</i>, <i>S.kow</i> - <i>Saccoglossus kowalevskii</i>, <i>T.cas</i> - <i>Tribolium castaneum</i>.