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

<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

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

<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

Details for used species, individuals and markers.

<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

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

<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

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

<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.

<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).

<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

Number of PALs (potentially amplifiable loci) for each of ten hardwood tree species.

<p>Hundreds to thousands of PALs were identified for each species sequenced. For all species the most commonly identified repeat motif was 2 bases, followed by 3 base motifs. Reptitive motifs of 4 bases were found the least often.</p

Identified repetitive elements and genes in genomic reads.

<p>The percent of reconstructed fragments with sequence similarity to known plant repetitive elements and gene sequences vary across species. The majority of identified repetitive elements originate from the retrotransposon classes of Gypsy and Copia.</p