Assembly result of the complete chloroplast (cp) genome sequence of <i>F</i>. <i>tataricum</i>.

<p>a. Three representative contigs (Ctgs) for the cp genome of tartary buckwheat and comparison with the corresponding regions of the common buckwheat cp genome. <b>b</b>. Mapping of WGS raw reads onto the completed cp sequence of tartary buckwheat. The principal structure of tartary buckwheat cp genome as represented by LSC, IRa, SSC, and IRb regions. Three representative Ctgs for the cp genome, Ctgs #3, #11, and #15, were arranged in an order based on BLASTZ analysis (<a href="http://nature.snu.ac.kr/tools/blastz_v3.php" target="_blank">http://nature.snu.ac.kr/tools/blastz_v3.php</a>) and overlapping between adjacent Ctgs. Blue and yellow bars indicate Ctgs matching the reference sequence in forward and reverse orientations, respectively, and the matching nucleotide positions are denoted at the reference cp sequence.</p

Comparison of the borders of LSC, SSC, and IR regions between the chloroplast genomes of two <i>Fagopyrum</i> species.

<p>a. <i>F</i>. <i>tataricum</i><b>. b.</b><i>F</i>. <i>esculentum</i>.</p

Comparison of chloroplast genome tandem repeats in <i>F</i>. <i>tataricum</i> and <i>F</i>. <i>esculentum</i>.

<p>^aIGS; Intergenic sequence, CDS; Coding sequence</p><p>^bLSC; Large Single Copy, IR; Inverted Repeat, SSC; Small Single Copy</p><p>Comparison of chloroplast genome tandem repeats in <i>F</i>. <i>tataricum</i> and <i>F</i>. <i>esculentum</i>.</p

Comparison of the complete chloroplast genome contents of <i>F</i>. <i>esculentum</i> and <i>F</i>. <i>tataricum</i>.

<p>Comparison of the complete chloroplast genome contents of <i>F</i>. <i>esculentum</i> and <i>F</i>. <i>tataricum</i>.</p

Confirmation of InDel regions between <i>F</i>. <i>esculentum</i> and <i>F</i>. <i>tataricum</i> germplasm chloroplast genome by PCR amplification.

<p>a, b, c, and d; PCR amplification with InDel #3, InDel #4, InDel #5 and InDel #6 region specific markers (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0125332#pone.0125332.s002" target="_blank">S2 Table</a>), respectively. M; 100 bp DNA ladder (Bioneer, Daejeon, South Korea). Solid line indicates <i>F</i>. <i>tataricum</i>, dotted line indicates <i>F</i>. <i>esculentum</i>.</p

Circular gene map of the <i>F</i>. <i>tataricum</i> chloroplast (cp) genome.

<p>Genes shown inside the circle are transcribed clockwise, and those outside the circle are transcribed counterclockwise.</p

Gene-specific Ks values between the chloroplast genomes of two <i>Fagopyrum</i> species (<i>F</i>. <i>tataricum</i> and <i>F</i>. <i>esculentum</i>).

<p>The Ks value was calculated with PAL2NAL. Four genes (<i>rpoC2</i>, <i>ycf3</i>, <i>accD</i>, and <i>clpP</i>) returned Ks values greater than 0.5, whereas the Ks values of the other genes were below 0.5.</p