Genome organisation.

<p>Here we show sections of the genomes (kilobases, kb) of <i>C</i>. <i>bombi</i> and <i>C</i>. <i>expoeki</i> (top two panels; (scaffold3_<i>4</i> and scf7180000000921, respectively) and the syntenic region in <i>L</i>. <i>major</i> (bottom panel) as an example of overall synteny among these genomes. Green arrows are gene sequences coding for proteins, as based on annotations in <i>L</i>. <i>major</i> 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 (<i>LmjF</i>.<i>34</i>.<i>0970</i> in <i>L</i>. <i>major</i>), which is an ortholog to gene Ce.1.39770 (<i>C</i>. <i>expoeki</i>) and Cb.1.06720 (<i>C</i>. <i>bombi</i>). 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 <i>C</i>. <i>bombi</i> scaffold.</p

Number and types of orthologs.

<p>Number and types of orthologs.</p

Putative N-glycan synthesis in <i>C</i>. <i>bombi</i>.

<p>(a) The complete N-glycan precursor synthesized in most eukaryotes (surrounded by dashed line) is composed of two <i>N</i>-acetylglucosamines (black squares), nine mannoses (white circles), and three glucoses (black circles). However, because <i>C</i>. <i>bombi</i> lacks <i>ALG6</i>, <i>ALG8</i>, <i>ALG10</i>, and <i>ALG12</i> genes, it was assumed that <i>C</i>. <i>bombi</i> 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 <i>C</i>. <i>bombi</i> genome, showing that these two enzymes are encoded by a fused gene on this scaffold 3/59. <b>(c)</b> Alignments of <i>Leishmania braziliensis</i> STT3 to a scaffold in <i>C</i>. <i>bombi</i> (scaffold 3/64).</p

Synteny.

<p>Synteny graph between <i>C</i>. <i>bombi</i> and <i>C</i>. <i>expoeki</i> genomes generated with SyMap 4.2 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0189738#pone.0189738.ref059" target="_blank">59</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0189738#pone.0189738.ref060" target="_blank">60</a>]. The plot shows all syntenic blocks between the scaffolds of <i>C</i>. <i>expoeki</i> (bottom half of the circle) mapping to scaffolds of <i>C</i>. <i>bombi</i> (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 <i>C</i>. <i>expoeki</i> scaffolds. For illustrative purposes, a few scaffolds (as named in this study) are indicated at their approximate position in the circle.</p

Phylogenetic relationships of orthologous proteins.

<p>Phylogenetic relationships of orthologous proteins in <i>C</i>. <i>bombi and C</i>. <i>exppoeki</i>, and as identified by OMA. Unrooted trees visualized with FigTree v.1.4.2 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0189738#pone.0189738.ref070" target="_blank">70</a>]; sequences from <i>C</i>. <i>bombi</i> (in red), and <i>C</i>. <i>expoeki</i> (in orange) shown in colour for clarity. Sequences of <i>Bodo saltans</i> (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) <i>gp63</i>-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) <i>amastin-</i>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).</p

Additional file 2: Table ST1. of Unity in defence: honeybee workers exhibit conserved molecular responses to diverse pathogens

List of 7,077 genes ordered by their rank product after the rank product analysis looking for up-regulated genes. Genes ordered from higher ranks (up-regulated) to lower ranks (non-regulated). Table ST2. List of 7,077 genes ordered by their rank product after the rank product analysis looking for down-regulated genes. Genes ordered from higher ranks (down-regulated) to lower ranks (non-regulated). Table ST3. List of 7,077 genes ordered by their rank product after the rank product analysis looking for differentially-regulated genes. Genes ordered from higher ranks (differentially-regulated) to lower ranks (non-regulated). Table ST4. List of 7,077 genes ordered by their rank product after the directed rank product analysis looking for up-regulated genes in abdominal tissue, after Nosema infection. Table ST5. List of 7,077 genes ordered by their rank product after the directed rank product analysis looking for down-regulated genes in abdominal tissue, after Nosema infection. Table ST6. Functional analysis (GO slim) based on top up-regulated genes in abdominal tissues (gut, fat body or all abdomen) upon infection by Nosema. Cut-off < 0.01 uncorrected p-value, genes from S4 Table. Table ST7. Functional analysis (GO slim) based on top down-regulated genes in abdominal tissues (gut, fat body or all abdomen) upon infection by Nosema. Cut-off < 0.01 uncorrected p-value, genes from S5 Table. Table ST8. List of 7,077 genes ordered by their rank product after the directed rank product analysis looking for up-regulated genes after RNA virus infection and Varroa infestation. Table ST9. List of 7,077 genes ordered by their rank product after the directed rank product analysis looking for down-regulated genes after RNA virus infection and Varroa infestation. Table ST10. Functional analysis (GO slim) based on top up-regulated genes upon infection by RNA virus and Varroa infestation. Cut-off < 0.01 uncorrected p-value, genes from S8 Table. Table ST11. Functional analysis (GO slim) based on top down-regulated genes upon infection by RNA virus and Varroa infestation. Cut-off < 0.01 uncorrected p-value, genes from S9 Table. Table ST12. List of the 209 highly connected (hub) genes with at least 34 inter-gene connections. Table ST13. List of genes involved in the immune gene network (Fig. 4C). Table ST14. List of immune genes used to construct the immune gene network (Fig. 4C). Table ST15. Experimental procedure and description of datasets. (XLSX 9947 kb

Additional file 1: Figure S1-S9. of Unity in defence: honeybee workers exhibit conserved molecular responses to diverse pathogens

This file includes supplementary figures documenting our multidimensional scaling analysis results, a heat map of the differential expression of the 7,077 genes across the 19 datasets, a Venn diagram of differentially expressed genes, the expression profile of the gene coding for hymenoptaecin, the distribution of genes according to their number of inter-gene connections, the degree of connectivity of differentially expressed genes, the process of gene selection for this study, the distribution of genes’ differential expression across datasets, and a diagram illustrating our new bioinformatics approach. (PDF 683 kb