Assorted primer combinations from this and prior studies.

<p><b>A</b>, “Universal barcode” primers are those described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0108581#pone.0108581-Kress3" target="_blank">[21]</a>. “LR barcode” primers are from a recent unpublished study. “JNV barcode” primers were developed in this study and were generated based on the microsatellite and barcode primers identified by the computational pipeline described in the text. These are indicated in the figure as the last four tracts, where “Zingiber” indicates the intraspecific <i>Z. officinale</i> and <i>Z. spectabile</i> comparison and “pan-Zing” indicates a comparison across all sequences described in this study. Underlined markers indicate multiple overlapping markers at that site. The blue and orange boxes demarcate the markers used to generate sequences in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0108581#pone-0108581-g003" target="_blank">Figure 3B and 3C</a>, respectively. <b>B</b> and <b>C</b>, Sequences from a range of Zingiberaceae species were amplified using the primer pairs indicated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0108581#pone-0108581-g003" target="_blank">Figure 3A</a>. <b>B</b> is associated with the blue box and shows products amplified by barcode set JNV-C (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0108581#pone.0108581.s006" target="_blank">Table S1</a>). <b>C</b> is associated with the orange box and shows products amplified by barcode set JNV-A (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0108581#pone.0108581.s006" target="_blank">Table S1</a>). Grey color indicates identity with the consensus of the alignment. Colored sites indicate a polymorphism, where different colors represent 4 different bases and light grey represents an ambiguous base. Appropriate regions from the fully sequenced plastomes were extracted and included in the alignment. These sequences are indicated by bold font. Names are not shown for samples that were not keyed to species-level.