Map of the mitochondrial genome of <i>B</i>. <i>oleracea</i> var. <i>capitata</i>.

<p>Boxes on the inside and outside of the outer circle represent ORF genes. Gene colors correspond to the functional categories listed in the legend. The inner circle displays the GC content represented by dark gray bars. The Fig was created using OGDraw v1.2 (adopted from [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194356#pone.0194356.ref045" target="_blank">45</a>]).</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

Statistics of <i>de novo</i> assembly of <i>Echinochloa</i> leaf transcriptomes.

<p>Statistics of <i>de novo</i> assembly of <i>Echinochloa</i> leaf transcriptomes.</p

A multiple alignment of plastid genome (KR233156) and four mtDNAs (KU831325, KJ820683, JF920286, and AP012988) of <i>Brassica oleracea</i> consists of several rearranged pieces.

<p>Each genome is laid out horizontally with homologous blocks represented as coloured rectangles. Regions inverted relative to plastid are set below those that match in the forward orientation. Lines collate aligned segments between plastid and different mtDNAs. Sections of white within blocks and gaps between blocks indicate lineage specific sequence.</p

Distribution of log₂ fold change of DEGs in pair-wise comparison; (A) EC-SNU1 vs. EC-SNU2, (B) EC-ENU1 vs. EC-ENU3, and (C) EC-SNU2 vs. EC-SNU3.

<p>Distribution of log₂ fold change of DEGs in pair-wise comparison; (A) EC-SNU1 vs. EC-SNU2, (B) EC-ENU1 vs. EC-ENU3, and (C) EC-SNU2 vs. EC-SNU3.</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

Whole-genome sequencing of <i>Brassica oleracea</i> var. <i>capitata</i> reveals new diversity of the mitogenome - Fig 4

<p>In the left panel (a) identification of variation in the KU831325 mtDNA in various inbred lines. A, B, and E are cabbage, C is broccoli, D is kale, F is cabbage of the Ogura CMS line, G is cauliflower, H is brussels sprouts, I is kohlrabi, and J is kailan and M is the reference ladder with 100 bp. The genotypes with the red asterisks were used for cloning, sequencing, and assemblage of mitochondrial DNA in <i>B</i>. <i>oleracea</i>. There are two bands for contig 2–3, with the lower band being the target amplified according to the primer product size presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194356#pone.0194356.t001" target="_blank">Table 1</a>. In right panel (b) showing relative expression with significant variation of different contigs/fragments present in different genotypes.</p

Molecular phylogenetic analysis by Maximum Likelihood method of the four <i>B</i>. <i>oleracea</i> mtDNAs according to the genomic sequences and the distribution of their contigs, the black coloured value is node length and blue coloured one is boost-strap value.

<p>Molecular phylogenetic analysis by Maximum Likelihood method of the four <i>B</i>. <i>oleracea</i> mtDNAs according to the genomic sequences and the distribution of their contigs, the black coloured value is node length and blue coloured one is boost-strap value.</p

The step-wise change of gene expression pattern in the phylogenetic relationship of three <i>E</i>. <i>crus-galli</i> accessions.

<p>The step-wise change of gene expression pattern in the phylogenetic relationship of three <i>E</i>. <i>crus-galli</i> accessions.</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