Fig. 1

Organization of the USP gene family in Platyhelminthes. a Platyhelminthes USP genes are distributed in clusters throughout the genome and show lineage-specific expansions and losses. For each species, the total number of USP genes are given in parentheses, followed by a scheme (boxes) showing the genomic organization for some genes. Boxes with blue frame correspond to syntenic genes in Cestoda species. The sequence alignment of the entire cluster in Cestoda parasites (50% of identity at baseline and using E. granulosus as the reference sequence) display high levels of sequence identity in the coding region. Gene identity of USP genes is lost when compared to the Trematoda and Turbellaria classes, suggesting a high divergence of the USP genes between groups. Some USP paralogs in the Cestoda were identified as pseudogenes (dotted, gripped, and striped boxes). Because of the synteny, pseudogenes in T. solium and Echinococcus spp. correspond to gene losses when compared to H. microstoma. The EgrG_ps1 pseudogene refers to the EgrG_2019 sequence (WormBase Parasite annotation). Asterisks indicate the same USP distribution for E. canadensis and E. multilocularis compared to E. granulosus, and for S. haematobium and O. viverrini compared to S. mansoni and C. sinensis, respectively. b The presence of indels (highlighted in red in the protein sequence) generates frameshift mutations and serves as evidence of a pseudogenization process. The sequences of some pseudogenes (EgrG_ps1, HmN_ps1) are very similar to that of their orthologs. Others (EgrG_ps2) are very different, and homologies are difficult to identify accurately by tBLASTn. In addition to the protein alignment, the indels are indicated in the coding sequence for three pseudogenes