Exploring the Schistosoma mansoni adult male transcriptome using RNA-seq

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 exo...

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Bibliographic Details
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
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Summary:	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.
Bibliography:	http://dx.doi.org/10.1016/j.exppara.2011.06.010 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0014-4894 1090-2449
DOI:	10.1016/j.exppara.2011.06.010