Additional file 1: Table S1. of Conservation and diversification of small RNA pathways within flatworms

C. elegans small non-coding RNA pathway genes used for homology search. Table S2. Ribonuclease III genes identified in flatworms. Table S3. Argonaute genes identified in flatworms. Table S4. microRNA pathway genes detected in flatworms. Table S5. Exogenous RNA interference pathway genes detected in flatworms. Table S6. Endogenous RNA interference pathway genes detected in flatworms. Table S7. Amplification pathway genes detected in flatworms. Table S8. RNA interference spreading signal genes detected in flatworms. Table S9. Chromatin remodeling genes associated to RNA interference detected in flatworms. (XLSX 47 kb

Additional file 2: Figure S1. of Conservation and diversification of small RNA pathways within flatworms

Dcr-2 and Dcr-3 genomic location and expression in Fasciolidae and Opisthorchiidae. In C. sinensis and O. viverrini genomes both paralogues are separated by less than 10 kb, while, in F. hepatica the intergenic region is almost 50 kb. Transcriptomic data of F. hepatica show that both genes are transcribed in several developmental stages. (TIFF 1513 kb

Additional file 3: Figure S2. of Conservation and diversification of small RNA pathways within flatworms

FL-Agos genomic location and expression in S. mansoni, F. hepatica and E. granulosus. Transcriptomic data show that all FL-Agos are expressed in several developmental stages. Genes size was found to be variable ranging from around 4 kb in E. granulosus to 6.5 kb in S. mansoni and almost 40 kb in one of the F. hepatica genes. (TIFF 5708 kb

Additional file 4: Figure S3. of Conservation and diversification of small RNA pathways within flatworms

Motifs detected in putative GW182 sequences of flatworms. Motifs detected in UBA and RRM domains are indicated in purple and lightblue boxes, respectively. The GW182 family conserved motif of AGO binding domain was also found in all flatworms (yellow box). Two additional motifs conserved only among flatworms were detected. The motif at the AGO binding domain (white box) is conserved in all flatworms, while, the other (black box) is rich in glutamine residues (Q) and is only conserved in trematodes and cestodes. Sequences of common motifs to all flatworm linages were aligned and residue conservation is indicated. Additionally, the number of GW repeats for each sequence are indicated. Species with parcial or no predicted gene model are not shown (see Additional file 1: Table S3). (TIFF 3464 kb

Additional file 5: Figure S4. of Conservation and diversification of small RNA pathways within flatworms

A maximum likelihood tree of RNA dependent RNA Polymerases. One hundred iterations bootstrap was calculated. Values below 0.4 are not shown. (TIFF 1023 kb

Evolutionary relationship among septins of humans and <i>Schistosoma mansoni</i>.

<p>Phylogenetic tree (based on Bayesian inference) generated from a multiple alignment of the conserved GTPase domains of septins from <i>S. mansoni</i> and two other informative protostomes and three deuterostomes. The numbers on the tree nodes are posterior probabilities calculated by MrBayes. Branches with the four discrete groups of septins are enclosed by the dotted lines. Species are identified by the small circles of different shapes and colors as indicated in the lower panel.</p

Superficial structures of miracidia and sporocysts of <i>Schistosoma mansoni</i>.

<p>Panels A and C represent a superficial cross section of miracidia and B and D depict a superficial layer of two-day-old sporocysts. The green panels A and B show F-actin stained with phalloidin conjugated with Alexa Fluor 568. The red panels C and D reveal septin structures labeled with anti-<i>Sm</i>SEPT10 immunoglobulin. The upper left inset in panel C highlights an epidermal plate of a miracidium, rich in septins, and in panel A the same region revealed a muscular structure stained with phalloidin. Scale bar, 20 µm.</p

Septins are ubiquitous in tissues of the schistosomulum.

<p>Cross section at an inner intersection of a schistosomulum cultured for 14 days. Panel A: Nuclei stained with DAPI. B: F-actin structure stained with phalloidin. C: Septin labeled with anti-<i>Sm</i>SEPT5. D: Merged channels. Scale bar, 20 µm.</p

Protonephridial ducts of the schistosome cercaria are septin rich structures.

<p>Optical section of cercariae labeled with phalloidin (green) and anti-<i>Sm</i>SEPT10 (red). The arrows indicate the flame cells at anterior termini of protonephridial canals. Scale bar, 20 µm.</p

Septin in germ cells of miracidia and sporocysts of schistosomes.

<p>Confocal optical sections of a miracidium (panel A) and a two day old sporocyst (B); nuclei stained with DAPI (blue) and actin filaments stained with phalloidin conjugated with Alexa Fluor 568 (green). Probing with anti-<i>Sm</i>SEPT10 immunoglobulin (red) revealed the prevalence of septin in germ cells of both miracidia and sporocysts. The insets of A and B highlight germ cell rich regions in these developmental stages. Scale bar, 20 µm.</p