14 research outputs found

    Marker <i>trn</i>DT visualized on a polyacrylamide gel.

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    <p>Lane 1: 50 bp ladder, lane 8: zero control, lane 2–7 and 13–14: analysis of wood-derived DNA, its location is inferred from genotypes, lane 9–12: references from North America (US), Europe (EU) or Asia (AS), respectively.</p

    Results of next-generation sequencing for oak reference assembly and polymorphism screening.

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    <p>Indexed individuals of oaks were sequenced using 150 bp paired-end reads and evaluated using <i>de novo</i> assembly (reference assembly). Pooled individuals were sequenced using 300 bp paired-end reads and evaluated using reference-guided assembly (polymorphism screen).</p

    List of primers for the amplification and resequencing of the newly developed markers.

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    <p>Fluorescent-labeling of the primers is given in column “sequences”: FAM = blue, VIC = green, PET = red. In the last column, the accession numbers of the related markers for the three species <i>Q</i>. <i>robur</i>, <i>Q</i>. <i>mongolica</i> and <i>Q</i>. <i>alba</i> are given. “Length” means sequence length.</p

    Phylogenetic relationship among chloroplast genomes of white oak species representing Old World and New World lineages.

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    <p>The best maximum likelihood tree is shown for four white oak chloroplast genomes (<i>Q</i>. <i>mongolica</i>; <i>Q</i>. <i>robur</i>; <i>Q</i>. <i>petraea</i>; <i>Q</i>. <i>alba</i>) and one outgroup genome (<i>Q</i>. <i>rubra</i>). Inferred branch lengths in maximum likelihood substitutions are shown in bold, and bootstrap support values are show in italics. The phylogenetic resolution of informative indel markers are shown in black inverted triangles, and the resolution of the diagnostic PCR-RFLP marker is shown as a grey triangle.</p

    PCR conditions compared for leaf and timber.

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    <p>Only the differences are shown, all other parameters are as given in material and methods.</p

    Fragment patterns of the five markers for individuals from Asia (top), North America (middle) and Europe (bottom).

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    <p>The sequence sizes for each peak as given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158221#pone.0158221.t003" target="_blank">Table 3</a> are shown beneath the peaks. The first blue peaks appear smaller (112, 120) than the sequenced length (115, 123) given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158221#pone.0158221.t003" target="_blank">Table 3</a>. The color code of the peaks is as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158221#pone.0158221.t002" target="_blank">Table 2</a>.</p

    Details for used species, individuals and markers.

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    <p>Given are number of individuals per species and continent tested with the five markers, and fragment length based on sequencing for each marker and species. Consensus sequences of the five markers are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158221#pone.0158221.s001" target="_blank">S1 Fig</a>.</p

    Expression patterns of tags StET010753 and StET009643 matching the tomato transaldolase isoforms ToTAL1 (PotTAL1) and ToTAL2, respectively.

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    <p>Tag StET10753 is weakly up regulated in the R1 and r1 plants but not in the ORF45 plants at three days post inoculation. Tag StET009643 shows clear up regulation only in the R1 plants one day after inoculation. Transcript levels are shown as mean tag counts/million of six (R1 and r1 plants), three (ORF45 plants at 0 dpi and 2 dpi) and two (ORF45 plants at 3 dpi) independent samples. Bars indicate the standard deviation according to the Poisson distribution.</p

    Categories of tag frequencies, fraction of unknown tags per category and number of tags matching one or more target sequences.

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    <p>(<b>A</b>) Histograms of the average tag frequencies. The curve above the histogram in <b>A</b> shows the average proportion (y-axis on the right) of unknown tags in the five frequency classes. (<b>B</b>) The number of tags matching from 1 to more than 15 different target sequences. NA: Number of tags with no match.</p
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