Figure 6

Genomic organization of HvOS2 in relation to its cereal homologues. A) Schematic view of gene bodies (exons plus introns) of five cereal MADS-I-like genes. Exons are depicted with orange boxes and introns with blue lines. Numbers on start and end of contigs refer to the length of particular genomic region. Length (bp) of first large introns is given under each intron. Regions within the first intron where retrotransposons were found are highlighted in red. B) Sequence similarity of the first introns of maize ZmB4FML1 and brachypodium Bradi2g59120 with 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: Left, full length maize retrotransposon Copia. PZMAY_CS_U68408_OPIE detected within the first intron of maize ZmB4FML1 and depicted in red; Right, the first intron of maize ZmB4FML1. The region of retrotransposon homology is shown in red. Bottom circle: Left, the brachypodium retrotransposon, Gypsy PBDIS_GX_ADDN0100106. Right, the first intron of brachypodium Bradi2g59120. Regions of homology are shown in red. Coding regions of retrotransposons integrase and reverse transcriptase are in purple and yellow-green, respectively. The 5’and 3’ LTR regions of retrotransposons are shown with bold black lines. Dark grey and light grey interconnecting ribbons depict regions of high and low similarity, respectively.