Exploring the Schistosoma mansoni adult male transcriptome using RNA-seq

• Published in: Experimental parasitology Vol. 132; no. 1; pp. 22 - 31
• Main Authors: Almeida, Giulliana Tessarin, Amaral, Murilo Sena, Beckedorff, Felipe Cesar Ferrarezi, Kitajima, João Paulo, DeMarco, Ricardo, Verjovski-Almeida, Sergio
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01-09-2012
• Subjects: adults; Animals; cDNA libraries; complementary DNA; Contig Mapping; Exons; Expressed Sequence Tags; Gene discovery; Gene Expression Regulation; genes; Genes, Helminth - genetics; Genes, Mitochondrial; Genome annotation; Genome, Helminth; High-Throughput Nucleotide Sequencing; landscapes; Male; males; Micro-exon genes; Molecular Sequence Data; non-coding RNA; parasites; parasitology; prediction; RNA, Helminth - chemistry; RNA-seq; Schistosoma japonicum - genetics; Schistosoma mansoni; Schistosoma mansoni - genetics; schistosomiasis; Sequence Alignment; Sequence Analysis, RNA; transcription (genetics); Transcriptome; Trematode; Micro-exon genes; Schistosoma mansoni; Genome annotation; Trematode; RNA-seq; Gene discovery
• ISSN: 0014-4894; 1090-2449
• DOI: 10.1016/j.exppara.2011.06.010

RNA-seq of Schistosoma mansoni adult male transcriptome provided high-quality sequence information to improve gene structure annotation [Display omitted]
► RNA-seq of Schistosoma mansoni adult male with 15×-deep coverage of transcribed genome bases. ► RNA-seq ESTs help to correct gene prediction exons in the genome annotation. ► Nine hundred and ninety predictions without previous evidence of expression were confirmed by ESTs. ► Intergenic and intronic genomic regions with novel evidence of transcription. ► Identification of 11 novel Micro-exon genes (MEGs).
Schistosoma mansoni is one of the agents of schistosomiasis, a chronic and debilitating disease. Here we present a transcriptome-wide characterization of adult S. mansoni males by high-throughput RNA-sequencing. We obtained 1,620,432 high-quality ESTs from a directional strand-specific cDNA library, resulting in a 26% higher coverage of genome bases than that of the public ESTs available at NCBI. With a 15×-deep coverage of transcribed genomic regions, our data were able to (i) confirm for the first time 990 predictions without previous evidence of transcription; (ii) correct gene predictions; (iii) discover 989 and 1196 RNA-seq contigs that map to intergenic and intronic genomic regions, respectively, where no gene had been predicted before. These contigs could represent new protein-coding genes or non-coding RNAs (ncRNAs). Interestingly, we identified 11 novel Micro-exon genes (MEGs). These data reveal new features of the S. mansoni transcriptional landscape and significantly advance our understanding of the parasite transcriptome.