A Comparison of Coding and Noncoding Sequences from Various MULEs

<div><p>(A) An alignment of the nucleotide sequence of a portion of the first exon, the first intron, and a portion of the second exon from the rice, <i>Setaria,</i> and sorghum MULEs. Identical nucleotides are displayed as periods; differences are as indicated.</p> <p>(B) An alignment of the 3' end of exon 2, intron 2, exon 3, intron 3, and the 5' end of exon 4 from <i>mudrA</i> homologs from rice <i>(Os493), S. faberi (Sf4),</i> and a related element from maize <i>(Zm890).</i> In both panels, amino acid translations, shaded for similarity to <i>Os493,</i> are portrayed below the nucleotide alignments. MURA sequence is provided for comparison.</p></div

Phylogenetic Analysis of Various <i>mudrA</i>-Homologous Sequences from Grasses Representative of Several Major Subfamilies of Grasses

<p>Species designations are as follows: Zm, <i>Zea mays</i> (MuDR is <i>mudrA</i>); Zl, <i>Zea luxurians;</i> Sv, <i>Setaria viridis;</i> Sa, <i>S. anceps;</i> Sf, <i>S. faberi;</i> Ss, <i>S. sphacelata;</i> Sg, <i>S. glauca;</i> Sp, <i>Setaria palmifolia;</i> Sb, <i>Sorghum bicolor;</i> Cl, <i>Coix lacryma;</i> Os, <i>O. sativa;</i> Pv, <i>P. virigatum;</i> Vz, <i>Vetevaria zizanoides;</i> Mr, <i>Muhlenberia rigens;</i> Mm, <i>Muhlenbergia macroura;</i> So, <i>Saccharum officinarum;</i> Sk, <i>Shibataea kumasaca;</i> Sn, <i>Sinarundinaria nitida;</i> As, <i>Avena sativa;</i> Ca, <i>Calamagrostis acutifolia;</i> Ta, <i>Triticum aestivum,</i> Hv, <i>Hordeum vulgare;</i> Am, <i>Ammophila arenaria;</i> Fr, <i>Festuca rubra;</i> Bm, <i>Briza maxima.</i> Numbers represent individual clones from each species, or the last three digits of the accession number if the sequence was obtained from NCBI. Colored blocks indicate major subfamilies: green, <i>Panicoideae</i>; blue, <i>Chloridoideae</i>; yellow, <i>Pooideae</i>; red, <i>Bambusoideae</i>. Branch lengths are proportional to distance, as indicated by the scale bar. Bootstrap support is as indicated for each branch.</p

DNA Gel Blots of Representative Species from All Major Subfamilies of the Grasses

<div><p>All blots were probed with a fragment of MULE <i>sf3</i> from <i>S. faberi.</i> Subfamilies (i.e., Pooideae) are as indicated.</p> <p>(A) 1, <i>Shibataea kumasaca;</i> 2, <i>Ehrharta erecta;</i> 3, <i>Oryza sativa indica;</i> 4, <i>Oryza sativa japonica;</i> 5, <i>Zizania latifolia;</i> 6, <i>Nardus stricta;</i> 7, <i>Diarrhena japonica;</i> 8, <i>Brachypodium sylvaticum;</i> 9, <i>Phalaris aquatica;</i> 10, <i>Hordeum vulgare;</i> 11, <i>Triticum aestivum;</i> 12, <i>Chasmanthium latifolium;</i> 13, <i>Andropogon gerardii;</i> 14, <i>Sorghum bicolor;</i> 15, <i>Tripsacum dactyloides;</i> 16, <i>S. faberi;</i> 17, <i>S. italica;</i> 18, <i>Zea mays;</i> 19, <i>Muhlenbergia rigens;</i> 20, <i>Eleusine indica;</i> 21, <i>Boutelova curtipendula;</i> 22, <i>Cortaderia jubata.</i></p> <p>(B) 1. <i>Zizania latifolia;</i> 2, <i>Shibataea kumasaca;</i> 3, <i>Chusquea montana;</i> 4, <i>Chusquea quila;</i> 5, <i>Sinarundinaria nitida;</i> 6, <i>Phyllostachys vivax;</i> 7, <i>Otatea acuminata;</i> 8, <i>Zeigotes</i> sp.; 9, <i>Brachypodium sylvaticum;</i> 10, <i>Zizania latifolium;</i> 11, <i>O. sativa (japonica);</i> 12, <i>S. faberi;</i> 13, <i>S. italica.</i></p> <p>(C) 1, <i>S. italica;</i> 2, <i>S. italica;</i> 3, <i>S. viridis;</i> 4, <i>S. faberi;</i> 5, <i>S. glauca;</i> 6, <i>S. anceps;</i> 7, <i>S. sphacelata;</i> 8, <i>O. sativa;</i> 9, <i>Zea mays.</i></p></div

Bar Graph Displaying Percent Similarity of the Setaria <i>(Sf4),</i> Maize <i>(Zm890),</i> and Sorghum <i>(Sb662)</i> Elements with the Rice Element <i>(Os493)</i>

<p>The region analyzed includes the last portion of exon 1, intron 1, portions of exon 2, intron 2, exon 3, intron 3, and the first portion of exon 4. Although percent similarity for exon 1 and intron 1 between <i>Sf4</i> and <i>Os493</i> is shown, the corresponding region in <i>Zm890</i> is not available, nor are sequences for the last two introns of <i>Sb662.</i> The percent figure is the percent identity of each element in the specified region to <i>Os493</i> in that region. Portions in which no sequence was available are given a 0% value. T Exon and T Intron refer to the sum of exons and introns, respectively, that were compared.</p

Bivariate biplot of W1-3 and W2-3 values of measurements from epidermal long cells of foxtail millet and green foxtail.

<p>W1-3 = width of undulated patterns of epidermal long cells of ΩIII; W2-3 = width of epidermal long cells of ΩIII. Error bar = SD.</p

Information on the plants studied.

<p>Information on the plants studied.</p

Comparison of undulated patterns of silicified epidermal long cells in different parts of the upper lemmas and paleas from foxtail millet and green foxtail.

<p>Comparison of undulated patterns of silicified epidermal long cells in different parts of the upper lemmas and paleas from foxtail millet and green foxtail.</p

Photographs of <i>Setaria</i> grains.

<p>1 = Z668, 2 = Z335, 3 = Z399, 4 = Z557, 5 = Z280, 6 = Z169, 7 = Z737, 8 = Z734, 9 = W28, 10 = Qing24, 11 = Qing68, 12 = Qing44, 13 = Qing46, 14 = Qing28, 15 = Qing7-1, 16 = Qing59.</p

Papillae distribution on surfaces of the upper lemmas from foxtail millet and green foxtail.

<p>Papillae distribution on surfaces of the upper lemmas from foxtail millet and green foxtail.</p

Classification results of discriminant analysis for ΩIII type phytolith.

<p>78.4% of foxtail millet and 76.9% of green foxtail are classified accurately.</p