37 research outputs found

    Comparison of putative TIS of different plants.

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    <p>The respective accession numbers: Yunnan82-114 (<i>S</i>. <i>spontaneum</i>) KX254601; 51NG3 (<i>S</i>. <i>robustum</i>) KX254591; Luohanzhe (<i>S</i>. <i>officinarum</i>) KX254598; <i>O</i>. <i>sativa</i> X54194; <i>Z</i>. <i>mays</i> X03990; <i>S</i>. <i>cereale</i> M37231; <i>T</i>. <i>aestivum</i> AJ315040; <i>M</i>. <i>sinensis</i> AJ238126; <i>C</i>. <i>sativus</i> X51542; <i>C</i>. <i>maxima</i> M28700; <i>C</i>. <i>pepo</i> X55960; <i>V</i>. <i>radiata</i> X17211; <i>V</i>. <i>faba</i> X16615; <i>S</i>. <i>mexicana</i> AJ489509; <i>B</i>. <i>juncea</i> X73032; <i>B</i>. <i>rapa</i> S78172; <i>B</i>. <i>oleracea</i> X60324; <i>A</i>. <i>thaliana</i> X52631; <i>R</i>. <i>sativus</i> Z11677; <i>N</i>. <i>tabacum</i> Y08422; <i>S</i>. <i>lycopersicum</i> AY366528; <i>S</i>. <i>tuberosum</i> AF464863; <i>C</i>. <i>annuum</i> HM352915; <i>O</i>. <i>europaea</i> AJ865373; <i>P</i>. <i>granatum</i> JX121275; <i>F</i>. <i>sylvatica</i> KC700362; <i>Q</i>. <i>suber</i> AY428812; <i>Q</i>. <i>petraea</i> EU555524; <i>Q</i>. <i>robur</i> EF208969.</p

    Physical mapping of IGS and pTa71 probe in Yunnan82-114 (<i>S</i>. <i>spontaneum</i>), 51NG3 (<i>S</i>. <i>robustum</i>) and Luohanzhe (<i>S</i>. <i>officinarum</i>).

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    <p>FISH with IGS (red- B, F, J), and wheat rDNA pTa71 probe (green- A, E, I) in meristematic root tip metaphase chromosomes of Yunnan82-114 (A-D), 51NG3 (E-H), and Luohanzhe (I-L). DNA is counterstained with DAPI (blue—C, G, K). The fourth column shows the merged images of both signals of IGS and wheat rDNA pTa71 probe and DAPI-stained chromosomes (D, H, L). Arrows indicate minor loci NORs (A, B, D; E, F, H; I, J, L). Scale bars = 5 μm.</p

    TaqMan PCR and conventional PCR for detection of asymptomatic (As) and symptomatic (S) pokkah boeng leaves from the field-grown sugarcane.

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    w<p>For quantitative TaqMan PCR reactions, two primer-probe combinations were used; FAM-gx1 is specific to <i>F. verticillioides</i>; FAM-gx2 specific to <i>F. proliferatum</i>.</p>y<p>For conventional PCR, two primer sets were used; Pgx1 is specific to <i>F. verticillioides</i>; Pgx2 specific to <i>F. proliferatum</i>. ‘+’ is positive; ‘−’ is negative.</p>z<p>NTC: Negative test control (water).</p

    Canonical structural organization of the IGS regions in (A) Yunnan82-114 (<i>S</i>. <i>spontaneum</i>), (B) 51NG3 (<i>S</i>. <i>robustum</i>) and (C) Luohanzhe (<i>S</i>. <i>officinarum</i>).

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    <p>IGS: intergenic spacer; TTS: transcription termination site; NTS: non-transcribed spacer; TIS: transcription initiation site; ETS: external transcribed sequence; SR: sub-repeat. CpG island: cytosine-guanine island.</p

    GISH analysis of the F<sub>1</sub> hybrids and BC<sub>1</sub> progeny.

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    <p><i>Saccharum</i> spp. chromosomes were visualized in red and <i>E</i>. <i>arundinaceus</i> chromosomes in green. (A) YCE 96-66 (F<sub>1</sub>): 29 chromosomes from <i>E</i>. <i>arundinaceus</i> and 40 chromosomes from <i>Saccharum</i> spp.; (B) YCE 01–102 (BC<sub>1</sub>): 22 chromosomes from <i>E</i>. <i>arundinaceus</i> and 96 chromosomes from <i>Saccharum</i> spp.; (C) YCE 01–36 (BC<sub>1</sub>): 36 chromosomes from <i>E</i>. <i>arundinaceus</i>, 96 chromosomes from <i>Saccharum</i> spp. and one terminally translocated chromosome; (D) YCE 01–61 (BC<sub>1</sub>): 31 chromosomes from <i>E</i>. <i>arundinaceus</i> and 85 chromosomes from <i>Saccharum</i> spp.; (E) YCE 01–69 (BC<sub>1</sub>): 31 chromosomes from <i>E</i>. <i>arundinaceus</i> and 88 chromosomes from <i>Saccharum</i> spp.; (F) YCE 01–92 (BC<sub>1</sub>): 35 chromosomes from <i>E</i>. <i>arundinaceus</i>, 95 chromosomes from <i>Saccharum</i> spp. and one terminally translocated chromosome. The arrowhead in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110390#pone-0110390-g001" target="_blank">Figure 1C</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110390#pone-0110390-g001" target="_blank">Figure 1F</a> shows the translocated chromosome. Scale bars: 5 µm.</p

    Comparative genetic analysis of the 45S rDNA intergenic spacers from three <i>Saccharum</i> species

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    <div><p>The 45S ribosomal DNA (rDNA) units are separated by an intergenic spacer (IGS) containing the signals for transcription and processing of rRNAs. For the first time, we sequenced and analyzed the entire IGS region from three original species within the genus <i>Saccharum</i>, including <i>S</i>. <i>spontaneum</i>, <i>S</i>. <i>robustum</i>, and <i>S</i>. <i>officinarum</i> in this study. We have compared the IGS organization within three original species of the genus <i>Saccharum</i>. The IGS of these three original species showed similar overall organizations comprised of putative functional elements needed for rRNA gene activity as well as a non-transcribed spacer (NTS), a promoter region, and an external transcribed spacer (ETS). The variability in length of the IGS sequences was assessed at the individual, intraspecies, and interspecies levels of the genus <i>Saccharum</i>, including <i>S</i>. <i>spontaneum</i>, <i>S</i>. <i>robustum</i>, and <i>S</i>. <i>officinarum</i>. The ETS had greater similarity than the NTS across species, but nevertheless exhibited variation in length. Within the IGS of the <i>Saccharum</i> species, base substitutions and copy number variation of sub-repeat were causes of the divergence in IGS sequences. We also identified a significant number of methylation sites. Furthermore, fluorescent <i>in situ</i> hybridization (FISH) co-localization of IGS and pTa71 probes was detected on all representative species of the genus <i>Saccharum</i> tested. Taken together, the results of this study provide a better insight into the structure and organization of the IGS in the genus <i>Saccharum</i>.</p></div

    Phylogenetic relationships among 15 accessions of the genus <i>Saccharum</i>.

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    <p>Bootstrap values from 1000 tests are indicated at the nodes. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The ML and NJ tree of the same data is topologically identical.</p

    Chromosome composition of the intergeneric BC<sub>2</sub> and BC<sub>3</sub> progeny between <i>Saccharum</i> spp. and <i>E</i>. <i>arundinaceus</i>.

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    <p><b>Note:</b> Since small variation of chromosome counts can occur due to the loss or the overlapping of a few chromosomes from the preparation, the modal number of chromosomes and the range of total numbers of chromosomes in 2n cell are presented for the sugarcane clones analyzed. S and E indicate <i>Saccharum</i> spp. chromosome and <i>E</i>. <i>arundinaceus</i> chromosome, respectively. S/E and E/S indicate <i>Saccharum</i> spp. centromere with <i>E</i>. <i>arundinaceus</i> chromosome segment and <i>E</i>. <i>arundinaceus</i> centromere with <i>Saccharum</i> spp. chromosome segment, respectively.</p><p>Chromosome composition of the intergeneric BC<sub>2</sub> and BC<sub>3</sub> progeny between <i>Saccharum</i> spp. and <i>E</i>. <i>arundinaceus</i>.</p
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