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Fig. 6 | Chinese Medicine

Fig. 6

From: An integrated study of Violae Herba (Viola philippica) and five adulterants by morphology, chemical compositions and chloroplast genomes: insights into its certified plant origin

Fig. 6

Analyses of sequences divergence. A Comparison of the LSC, IR, and SSC junctions. Colored boxes for genes represent the gene position. JLB denotes the LSC/IRb junction, JSB denotes the SSC/IRb junction, JSA denotes the SSC/IRa junction, and JLA denotes the LSC/IRa junction. B Global alignment of six Viola cp genomes using the annotation of V. inconspicua as a reference. Dark blue blocks indicate exons, and red blocks indicate conserved non-coding sequences (CNS). tRNA and rRNA genes are denoted by cyan blocks. White peaks represent regions with sequence variation among cp genomes. Arrows are drawn above the graph pointing the direction of genes. 70% cut-off was used for the plot, and the vertical axis indicates sequence identity between 50 and 100%. The red rectangle frames indicate the divergent hotspot regions. C Sliding window analysis of the complete cp genomes of six Viola species (window length: 800 bp, step size: 200 bp). X-axis indicates the midpoint of windows. Y-axis indicates nucleotide diversity (Pi) within each window. And the red line indicates the threshold for potential genetic markers (Pi threshold = 0.015). Regions with Pi values meet or exceed 0.015 were marked out on the graph. The multicolored legend above shows the gene order

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