Identification of Transposable Elements in Schistosoma mansoni.

Transposable elements (TEs) represent a significant portion of eukaryotic genomes and are important players in their dynamics and evolution. Therefore, the description of TEs and the analysis of their distribution in the genomes are important steps to understand their influence in the architecture of genomes. Here we describe the protocol used by us to identify and curate consensus TEs sequences from S. mansoni, as well the protocol to map these elements in the S. mansoni genome. We expect that these protocols may help researchers interested in studying TEs content in S. mansoni or other organisms.

Impact of transposable elements in the architecture of genes of the human parasite Schistosoma mansoni.

The parasites belonging to the genus Schistosoma are agents of schistosomiasis, a disease estimated as affecting 235 million people in the world. To better understand the structure of Schistosoma mansoni genome, transposable elements (TEs) distribution and impact on gene structures were investigated. Our analyses indicated a differential distribution of TEs throughout the gene structure. Introns located at the 5' end of the genes are less prone to display TEs and introns lacking TEs tend to be shorter. Therefore, this could be one of the factors explaining previous data showing that S. mansoni displays shorter introns near the 5' end of the genes. Identification of six genes harboring TEs in their coding region suggests a positive contribution for the evolution of proteome repertory of S. mansoni. Taken together, our data suggest significant contributions of TEs to the architecture of genes from S. mansoni.

Distribution patterns and impact of transposable elements in genes of green algae.

Transposable elements (TEs) are DNA sequences able to transpose in the host genome, a remarkable feature that enables them to influence evolutive trajectories of species. An investigation about the TE distribution and TE impact in different gene regions of the green algae species Chlamydomonas reinhardtii and Volvox carteri was performed. Our results indicate that TEs are very scarce near introns boundaries, suggesting that insertions in this region are negatively selected. This contrasts with previous results showing enrichment of tandem repeats in introns boundaries and suggests that different evolutionary forces are acting in these different classes of repeats. Despite the relatively low abundance of TEs in the genome of green algae when compared to mammals, the proportion of poly(A) sites derived from TEs found in C. reinhardtii was similar to that described in human and mice. This fact, associated with the enrichment of TEs in gene 5' and 3' flanks of C. reinhardtii, opens up the possibility that TEs may have considerably contributed for gene regulatory sequences evolution in this species. Moreover, it was possible identify several instances of TE exonization for C. reinhardtii, with a particularly interesting case from a gene coding for Condensin II, a protein involved in the maintenance of chromosomal structure, where the addition of a transposomal PHD finger may contribute to binding specificity of this protein. Taken together, our results suggest that the low abundance of TEs in green algae genomes is correlated with a strict negative selection process, combined with the retention of copies that contribute positively with gene structures.

Accelerated evolution of schistosome genes coding for proteins located at the host-parasite interface.

Study of proteins located at the host-parasite interface in schistosomes might provide clues about the mechanisms utilized by the parasite to escape the host immune system attack. Micro-exon gene (MEG) protein products and venom allergen-like (VAL) proteins have been shown to be present in schistosome secretions or associated with glands, which led to the hypothesis that they are important components in the molecular interaction of the parasite with the host. Phylogenetic and structural analysis of genes and their transcripts in these two classes shows that recent species-specific expansion of gene number for these families occurred separately in three different species of schistosomes. Enrichment of transposable elements in MEG and VAL genes in Schistosoma mansoni provides a credible mechanism for preferential expansion of gene numbers for these families. Analysis of the ratio between synonymous and nonsynonymous substitution rates (dN/dS) in the comparison between schistosome orthologs for the two classes of genes reveals significantly higher values when compared with a set of a control genes coding for secreted proteins, and for proteins previously localized in the tegument. Additional analyses of paralog genes indicate that exposure of the protein to the definitive host immune system is a determining factor leading to the higher than usual dN/dS values in those genes. The observation that two genes encoding S. mansoni vaccine candidate proteins, known to be exposed at the parasite surface, also display similar evolutionary dynamics suggests a broad response of the parasite to evolutionary pressure imposed by the definitive host immune system.