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https://www.arca.fiocruz.br/handle/icict/7836
A SYSTEMATICALLY IMPROVED HIGH QUALITY GENOME AND TRANSCRIPTOME OF THE HUMAN BLOOD FLUKE SCHISTOSOMA MANSONI
genes expression
genomics databases
genomics libraries
invertebrates genomics
parasitic life cycles
Schistosoma mansoni
sequence assembly
Author
Protasio, Anna V.
Tsai, Isheng J.
Babbage, Anne
Nichol, Sarah
Hunt, Martin
Aslett, Martin A.
Silva, Nishadi de
Velarde, Giles S.
Clark, Richard C.
Davidson, Claire
Dillon, Gary P.
Holroyd, Nancy E.
Lloyd, Christine
McQuillan, Jacquelline
Otto, Thomas D.
Quail, Michael A.
Berriman, Matthew
Anderson, Tim J. C.
LoVerde, Phillip Thomas
Oliveira, Guilherme Corrêa de
Zerlotini, Adhemar
Manuel, Sophia J. Parker
Wilson, R. Alan
Dunne, David W.
Tsai, Isheng J.
Babbage, Anne
Nichol, Sarah
Hunt, Martin
Aslett, Martin A.
Silva, Nishadi de
Velarde, Giles S.
Clark, Richard C.
Davidson, Claire
Dillon, Gary P.
Holroyd, Nancy E.
Lloyd, Christine
McQuillan, Jacquelline
Otto, Thomas D.
Quail, Michael A.
Berriman, Matthew
Anderson, Tim J. C.
LoVerde, Phillip Thomas
Oliveira, Guilherme Corrêa de
Zerlotini, Adhemar
Manuel, Sophia J. Parker
Wilson, R. Alan
Dunne, David W.
Affilliation
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Texas Biomedical Research Institute. San Antonio, TX, United States of America
University of Texas Health Science Center. Departments of Biochemistry and Pathology. San Antonio, TX, United States of America
Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Centro de Excelência em Bioinformatica. Belo Horizonte, MG, Brazil/Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Genomics and Computational Biology Group. Belo Horizonte, Minas Gerais, Brazil/Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. National Institute for Science and Technology in Tropical Diseases. Belo Horizonte, Minas Gerais, Brazil
Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Centro de Excelência em Bioinformatica. Belo Horizonte, MG, Brazil
University of York. Department of Biology. Heslington, York, United Kingdom
University of York. Department of Biology. Heslington, York, United Kingdom
University of Cambridge. Department of Pathology. Cambridge, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Wellcome Trust Sanger Institute. Wellcome Trust Genome Campus. Hinxton, United Kingdom
Texas Biomedical Research Institute. San Antonio, TX, United States of America
University of Texas Health Science Center. Departments of Biochemistry and Pathology. San Antonio, TX, United States of America
Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Centro de Excelência em Bioinformatica. Belo Horizonte, MG, Brazil/Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Genomics and Computational Biology Group. Belo Horizonte, Minas Gerais, Brazil/Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. National Institute for Science and Technology in Tropical Diseases. Belo Horizonte, Minas Gerais, Brazil
Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Centro de Excelência em Bioinformatica. Belo Horizonte, MG, Brazil
University of York. Department of Biology. Heslington, York, United Kingdom
University of York. Department of Biology. Heslington, York, United Kingdom
University of Cambridge. Department of Pathology. Cambridge, United Kingdom
Abstract
Schistosomiasis is one of the most prevalent parasitic diseases, affecting millions of people in developing countries. Amongst the human-infective species, Schistosoma mansoni is also the most commonly used in the laboratory and here we present the systematic improvement of its draft genome. We used Sanger capillary and deep-coverage Illumina sequencing from clonal worms to upgrade the highly fragmented draft 380 Mb genome to one with only 885 scaffolds and more than 81% of the bases organised into chromosomes. We have also used transcriptome sequencing (RNA-seq) from four time points in the parasite's life cycle to refine gene predictions and profile their expression. More than 45% of predicted genes have been extensively modified and the total number has been reduced from 11,807 to 10,852. Using the new version of the genome, we identified trans-splicing events occurring in at least 11% of genes and identified clear cases where it is used to resolve polycistronic transcripts. We have produced a high-resolution map of temporal changes in expression for 9,535 genes, covering an unprecedented dynamic range for this organism. All of these data have been consolidated into a searchable format within the GeneDB (www.genedb.org) and SchistoDB (www.schistodb.net) databases. With further transcriptional profiling and genome sequencing increasingly accessible, the upgraded genome will form a fundamental dataset to underpin further advances in schistosome research.
Keywords
DNA sequencesgenes expression
genomics databases
genomics libraries
invertebrates genomics
parasitic life cycles
Schistosoma mansoni
sequence assembly
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