Figure 1.
Graphical circular map of the apicoplast genome of B. microti R1 isolate.
The map was designed using CGview and GenomeVx. From outside to center: coding sequence (CDS), % G+C, GC skew and base coordinates. hypA-E refer to five hypothetical protein encoding genes found in the apicoplast genome of B. microti.
Figure 2.
Schematic representation of gene clusters in the apicoplast genomes of various apicomplexan parasites.
Comparison was performed using Mauve and BLAST analyses. The red and blue bars between chromosomal DNA sequences represent highly conserved regions in the forward and reverse directions respectively. Only highly conserved and syntenic regions were included in the present analysis. tRNA genes are marked by *.
Figure 3.
Gene organization of cluster 1 in the apicoplast genomes of B. microti (R1), B. bovis (T2Bo), P. falciparum (3D7), T. gondii and T. parva (Mugaga) and the chloroplast genome of Chromera sp. (CCMP3155).
Light grey boxes represent highly divergent genes. White boxes corresponds to genes restricted to one species.
Figure 4.
Schematic representation of the DNA regions surrounding cluster 1 in B. microti R1, B. bovis T2Bo and T. parva Mugaga.
A line connecting the two ends of Cluster 1 indicate possible recombination events accounting for differences found in the gene organization and size between apicoplast genomes of piroplasmida.
Figure 5.
Domain structure and organization of Cluster 2 genes in B. microti and other apicomplexan parasites.
A. Comparison of ClpC domain structure between B. microti, P. falciparum, T. gondii and Chromera sp. B. microti apicoplast genome encodes two ClpC proteins that lack the N-terminus part as revealed by Pfam and TMpred predictions. Other apicomplexan ClpC structures have been obtained from Pfam database using UNIPROT accession numbers. Two PfamA domains are found in ClpC proteins of apicomplexa: AAA_2 (ATPase catalytic function) and ClpB_D2-small (conserved C-terminal domain). Light grey boxes indicate regions of low complexity. Transmembrane domains were predicted by Pfam only for T. gondii ClpC proteins (TM). B. Gene organization of cluster 2. The tRNA genes of cluster 2, which are conserved in all three apicoplast genomes are in bold. Three putative genes, C, D and E present at 3′ end of B. microti cluster 2 have no significant homologies with each other and lack homologs in other parasites.
Figure 6.
Organization and evolution of the rDNA region in the apicoplast genome of B. microti and other apicomplexa.
A. Phylogenetic analysis based on ssu and lsu genes. The tree was obtained using the maximum-likelihood method with (Bootstrap over 90%). Genomic organization of rDNA regions in the apicoplast or chloroplast genomes is given on top of each branch. B. Gene organization of the rDNA regions. The tRNA genes that are present in all apicomplexan genomes are shown in bold. Scale bar represents the number of substitutions per site.
Figure 7.
Summary of the evolution of the organization of the apicoplast genome in apicomplexan parasites.
The unweighted tree was built using raw data from Figure S2 in File S1. The branch supporting the clade piroplasmida is associated with several major genomic rearrangements. *: events that occurred twice in the apicoplast evolution; +: rearrangement, duplication and insertion events observed in B bovis and T. parva involving distinct genes.