Phylogenies of plastid genomes of green algae, euglenids and <i>Bigelowiella</i> based on 70 genes.

<p><b>A.</b> This phylogenetic tree was constructed using the maximum likelihood method implemented in RAxML, using the LG+I+G model selected by ProtTest. The bootstraps were estimated in 500 replicates. <b>B.</b> This tree was constructed in Beast v 1.6.1 using the WAG+I+Γ model of substitution and an uncorrelated exponential model of relaxed molecular clock. MCMCs were run for 10*10⁶ generations; trees from the first 2*10⁶ generations were discarded as the burn-in. Node labels represent posterior probabilities, node bars represent the 95% confidence interval of relative node ages.</p

Simplified maps of the plastid genomes of <i>Eutreptiella gymnastica</i>, <i>Euglena gracilis</i>, <i>Euglena longa</i> and <i>Pyramimonas parkeae</i>.

<p>The maps are in scale to their sizes. The colors indicate the coding strands (plus-green and minus-violet), the ribosomal RNAs (blue) and introns (yellow). The inverted repeats IRA and IRB in <i>Pyramimonas</i> and <i>Eutreptiella</i> are marked in red. The ori site in <i>Euglena gracilis</i> is marked by an arrow.</p

General features of euglenid and <i>Pyramimonas</i> cpDNA.

<p>General features of euglenid and <i>Pyramimonas</i> cpDNA.</p

Venn diagrams showing overlaps in protein coding capacities between known euglenid plastid genomes and the plastid genome of <i>Pyramimonas parkeae</i>.

<p>The schematic representation of genome relationships is indicated in the left. Arrows indicate the probable fate of the genes absent from euglenid genomes. The genes are colour coded in respect to the functional group of their products: housekeeping proteins (black), proteins involved in photosynthesis (green), maturases of introns (red) and genes with unknown function (gray). Maturases of introns included in the phylogenetic tree of maturases (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033746#pone.0033746.s001" target="_blank">Figure S1</a>) are marked by asterisks.</p