Maximum Likelihood phylogenetic tree of the tribe Hyoscyameae based on 10 chloroplast markers (11,610 bp).

<p>Taxa in red contain the <i>cox1</i> intron and CCT (co-conversion tract); taxa in light blue lack the <i>cox1</i> intron; taxa in black were not tested for the <i>cox1</i> intron. Filled and empty squares indicate taxa with and without an inversion in the intergenic region <i>trnC-psbM</i>, respectively. Numbers represent support values: 100 bootstrap (BS) replicates of ML analysis (top left), 1000 bootstrap replicates of MP analysis (top right) and posterior probabilities (PP) of Bayesian Inference (bottom). BS values and PP are shown when >50% and >0.9, respectively.</p

Identity plots comparing <i>Hyoscyamus niger</i> chloroplast genome to other Solanaceae.

<p>Pairwise comparisons and sequence identity between <i>Hyoscyamus niger</i> and five solanaceous chloroplast genomes for selected regions using the VISTA program. The Y-axis represents the % identity (50–100%) across the chloroplast genome. Coding and non-coding regions are marked in green and blue, respectively. Pink boxes indicate known (empty boxes) and novel (filled boxes) plastid regions used in the phylogenetic analyses in this study.</p

Alternative hypotheses for the evolution of the <i>cox1</i> intron and CCT in the tribe Hyoscyameae.

<p>Proposed evolutionary relationships within the tribe Hyoscyameae, showing intron acquisition (filled circle) by horizontal gene transfer. Taxa in red contain the <i>cox1</i> intron and CCT (co-conversion tract); taxa in light blue lack the <i>cox1</i> intron and CCT. <b>A.</b> Evolutionary hypothesis showing two independent intron acquisitions (homoplasious character) within the tribe. <b>B.</b> Evolutionary hypothesis based on a single intron acquisition (synapomorphy) within the tribe.</p

Chloroplast genome of <i>Hyoscyamus niger</i>.

<p>Large and small single copy regions (LSC, SSC) and inverted repeats (IR) are indicated. Intron-containing genes are in bold face. Genes drawn inside and outside the circle are transcribed clockwise and counterclockwise, respectively. Genes belonging to different functional groups are marked with colors. Internal circle shows the %GC content across the cpDNA. A line is shown at GC content of 50%.</p