Figure 3

Genomic analysis of cereal DME genes. A) Schematic view of cereal HvDME (FM164415), BdDME (Bradi4g08870), OsDME (01 g11900.1) and ZmDME (GRMZM2G123587) genes. Exons are depicted with orange boxes and introns with blue lines. 3’ untranslated regions are shown as light blue lines. Regions within the 3’ untranslated region of HvDME and within the intron of ZmDME where retrotransposon sequences were found are highlighted in red. B) Sequence similarity of HvDME and ZmDME with Copia retrotransposons, visualized in Circoletto (http://tools.bat.ina.certh.gr/circoletto/) after blast analysis with MASiVE (http://tools.bat.ina.certh.gr/masive/) and LTRphyler (http://tools.bat.ina.certh.gr/ltrphyler/). Upper circle: Full length HvDME gene (left); the Copia PTAES_CS_cons_maximus Sirevirus retrotransposon (right). The 5’ and 3’ LTR regions of the retrotransposon are shown with bold black lines. The regions of retrotransposon homology between the LTRs and the 3’ downstream region of HvDME are marked in red. Lower circle: Full length ZmDME1 gene (right); the maize Copia Ji Sirevirus retrotransopson element in different chromosomal locations of the maize genome (left). The ZmDME gene resides at the Zmay_chr_5_D_1618643 site (chromosome 5, sense strand, position 1618643 bp from the chromosomal start). Regions of homology are shown in red. Coding regions of retrotransposon integrase and reverse transcriptase are in purple and yellow-green, respectively. Dark-grey and light- grey interconnecting ribbons depict regions of high and low similarity, respectively.