Clustering of Schistosoma mansoni mRNA sequences and analysis of the most transcribed genes: implications in metabolism and biology of different developmental stages

Abstract

Key words: Schistosoma mansoni -bioinformatics -expressed sequences tag -clustering analysis -metabolismSchistosoma mansoni is a dioiceous trematode and one of the etiologic agents of schistosomiasis, the second more significant tropical disease concerning public health. Despite recent efforts undertaken to contain its progress, the disease is still endemic in several countries, with around 200 million people infected by the parasite (http://www.who.int/ctd/schisto/epidemio.htm). The study of S. mansoni is, therefore, very important in human parasitology. Gaining knowledge on the genome of this parasite is essential for a better understanding of its metabolism and biology and will help to elucidate important aspects of the mechanisms of drug resistance and antigenic variation that allow it to escape from the host immune system (Franco et al. 2000).The size of S. mansoni genome is estimated in 270Mb with the number of expressed genes ranging from 15000 to 20000 (Simpson et al. 1982, Franco & Simpson 2001. Although some genomic sequences of S. mansoni have been produced, the Schistosoma Genome Network (SGN) has chosen as first priority the sequencing of cDNA using the expressed sequence tags (ESTs) strategy, from which is possible to obtain fast and relevant information Although resulting in fast and very important information, ESTs available from public databases, such as dbEST, show some degree of redundancy and present a great number of errors, because they are single pass sequences (Miller et al. 1999). To overcome these problems and to increase the length of the sequences, facilitating identification by homology searches, clustering procedures are performed (Oliveira & Johnston 2001). In this kind of procedure, sequences that have some region of similarity are joined into a cluster. Therefore, sequences possessing overlapping regions and representing a single gene are joined into the same cluster, decreasing redundancy. Sequences of each cluster are then aligned to generate a consensus sequence. In this approach, the base (and, if available, the quality value designated by the base caller program) present in each sequence position is considered in the construction of a high quality consensus (Huang & Madan 1999). The clustering procedure can, therefore, have two outcomes: consensus are generated by the alignment of the sequences of a cluster and singlets result from sequences that have not been grouped to any others. Theoretically, each sequence (either a consensus or a singlet) should represent an individual gene, and so, these sequences are called uniques. As is expected that each sequence represents a single gene, the comparison of the number of uniques with the total number of predicted genes make it possible to know, approximately, how many genes have not been discovered yet.

Development of Multiplex PCR Assays for the Identification of the 33 Serotypes of Streptococcus suis

“…Each cps gene was compared to the local database using the BLASTn program with default parameters. The E-value cut off for a significant match was set at 10 −10 [46]. Serotype-specific genes were identified when the BLAST results showed no similarity to sequences of other serotype strains.…”

The cytoskeleton and motor proteins of human schistosomes and their roles in surface maintenance and host–parasite interactions

“…Expressed sequence tag (EST) datasets of schistosomes are dominated by transcripts encoding cytoskeletal and motor proteins, (6)(7)(8) probably reflecting the high transcriptional activity of genes encoding these molecules in all life-cycle stages. Not only do cytoskeletal molecules dominate in the parasite transcriptome, but they are also implicated in many host-parasite interactions.…”

Signal transduction in larval trematodes: putative systems associated with regulating larval motility and behaviour

“…As mentioned previously, the recently published EST sequencing and annotation projects for S. mansoni (Verjovski-Almeida et al 2003) and S. japonicum (Hu et al 2003), representing a significant sampling of the complete transcriptomes of these two major schistosome species, as well as other schistosome gene expression studies (Santos et al 1999 ;Franco et al 2000 ;Prosdocimi et al 2002 ;Merrick et al 2003), provide excellent resources for identifying genes related to potential signalling networks. As mentioned previously, the recently published EST sequencing and annotation projects for S. mansoni (Verjovski-Almeida et al 2003) and S. japonicum (Hu et al 2003), representing a significant sampling of the complete transcriptomes of these two major schistosome species, as well as other schistosome gene expression studies (Santos et al 1999 ;Franco et al 2000 ;Prosdocimi et al 2002 ;Merrick et al 2003), provide excellent resources for identifying genes related to potential signalling networks.…”

“…Identification of gene homologues, representing potential orthologues, of signal transduction molecules and their receptors represents an effective methodological approach to determining whether or not trematodes possess the basic molecular machinery required for various specific functional signalling systems. As mentioned previously, the recently published EST sequencing and annotation projects for S. mansoni (Verjovski-Almeida et al 2003) and S. japonicum (Hu et al 2003), representing a significant sampling of the complete transcriptomes of these two major schistosome species, as well as other schistosome gene expression studies (Santos et al 1999 ;Franco et al 2000 ;Prosdocimi et al 2002 ;Merrick et al 2003), provide excellent resources for identifying genes related to potential signalling networks. For S. japonicum, the majority of the annotated ESTs was derived from adult worms, and therefore contained little direct information on larval stage expression.…”