Fig. 3

Relationship between USP sequence modifications and gene expression patterns. a The gene expression profile is highly variable between the different life cycle stages of Cestoda and Trematoda species, with some USP genes with null or very low expression (EgrG_08734, EgrG_08735 and orthologs), others expressed in specific manner (EgrG_08111; EgrG_07797 and orthologs), and others constitutively expressed (EgrG_08738 and orthologs). ID numbers in red color refer to USP proteins that exhibit modifications in the ATP binding motif. The asterisk refers to the “ancestral” USPs (see Fig. 2). b USP sequence variations in the Platyhelminthes. On top, sequence logo generated with all USP sequences without changes to the ATP binding motif [Gx2Gx9G(S/T)]. Amino acids interacting with ligands are shown in boxes. Below, alignment of USP protein sequences showing modifications in the protein motif. ID numbers (in red) refer to USP proteins for which RNA-seq data was available, to facilitate the comparison between sequence modification and gene expression patterns. Modifications in the [Gx2Gx9G(S/T)] motif and at other sites known to be involved in ligand interaction are highlighted in red and yellow, respectively. The sequence of the Methanococcus jannaschii USP MJ0577 USP was used as a reference (starting from position 6), with the ATP binding motif highlighted in green. The residues under functional divergence are indicated by arrows (black arrows, residues shared by Cestoda and Trematoda; gray arrows: residues specific to the Cestoda or Trematoda) (see Table 1). c qPCR gene expression analysis of USP genes in the pre-adult form of E. ortleppi. Some genes (E0_08736, Eo_08738, Eo_07797, and Eo_10769) showed higher levels of gene expression than others (Eo_08734 and Eo_08735), in line with previously published RNA-seq data for the genus Echinococcus (see above). Asterisks indicate a p-value < 0.01 for the comparison of Eo_08734 and Eo_08735 with the other genes