Table 1.
Genome assembly statistics.
Fig 1.
Here we show sections of the genomes (kilobases, kb) of C. bombi and C. expoeki (top two panels; (scaffold3_4 and scf7180000000921, respectively) and the syntenic region in L. major (bottom panel) as an example of overall synteny among these genomes. Green arrows are gene sequences coding for proteins, as based on annotations in L. major and as indicated at the bottom. Reversed (left-facing) arrows indicate polycistronic regions. Note that, in this example, no introns are present. The red arrow refers to the amastin-like protein (LmjF.34.0970 in L. major), which is an ortholog to gene Ce.1.39770 (C. expoeki) and Cb.1.06720 (C. bombi). Two further amastin-like proteins are immediately up- and downstream from this location. The grey bars connect orthologs within the same orthologous group, as based on the OA analysis, and demonstrate a high degree of synteny among the three species. The yellow zone represents a gap in the C. bombi scaffold.
Fig 2.
Synteny graph between C. bombi and C. expoeki genomes generated with SyMap 4.2 [59,60]. The plot shows all syntenic blocks between the scaffolds of C. expoeki (bottom half of the circle) mapping to scaffolds of C. bombi (upper half of the circle). Each coloured block indicates a scaffold of the respective genome. Syntenic blocks are linked with lines in the colour of the C. expoeki scaffolds. For illustrative purposes, a few scaffolds (as named in this study) are indicated at their approximate position in the circle.
Fig 3.
Pie diagrams of the GO-categories for the genes annotated here.(a) C. bombi, (b) C. expoeki. The analysis was done with Blast2GO [61]. Only terms with more than 100 members are shown here.
Table 2.
Number and types of orthologs.
Fig 4.
The Venn diagrams show the number of orthologs that are shared among a set of five species. Calculated with the OMA browser; matches of all types (1:1, many:1, 1:many, and many:many) are included.
Fig 5.
Phylogenetic relationships of orthologous proteins.
Phylogenetic relationships of orthologous proteins in C. bombi and C. exppoeki, and as identified by OMA. Unrooted trees visualized with FigTree v.1.4.2 [70]; sequences from C. bombi (in red), and C. expoeki (in orange) shown in colour for clarity. Sequences of Bodo saltans (Kinetoplastida, Bodonidae; in bold black) represent a distant, outgroup kinetoplastid. Labels are as in TriTryp data base, and as named here for the two species under study. Branch values are posterior probabilities (PP), only values of PP < 1 shown here, all other cases have reported PP = 1. The horizontal bar is relative number of mutations per site. (a) gp63-like proteins. A total of 80 aligned, orthologous sequences were subjected to MrBayes (default settings, with 11 Mio generations and 25% burn-in fraction; convergence, S.D. of split frequencies < 0.004) to construct the consensus tree shown here. (b) amastin-like proteins. Tree from aligned, orthologous sequences submitted to MrBayes (default settings, 25% burn-in, with 12.6 Mio generations; convergence, S.D. of split frequencies = 0.01).
Fig 6.
Putative N-glycan synthesis in C. bombi.
(a) The complete N-glycan precursor synthesized in most eukaryotes (surrounded by dashed line) is composed of two N-acetylglucosamines (black squares), nine mannoses (white circles), and three glucoses (black circles). However, because C. bombi lacks ALG6, ALG8, ALG10, and ALG12 genes, it was assumed that C. bombi synthesizes biantennary DolPP-GlcNAc2Man7 (grey box, surrounded by solid line). Genes encoding ALG glycosyltransferases responsible for the addition of each carbohydrate are shown in italics together with linkage information. (b) Alignment of yeast Alg13 and Alg14 to a scaffold in the C. bombi genome, showing that these two enzymes are encoded by a fused gene on this scaffold 3/59. (c) Alignments of Leishmania braziliensis STT3 to a scaffold in C. bombi (scaffold 3/64).