A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni.
Autor(a) principal: | |
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Data de Publicação: | 2012 |
Outros Autores: | , , , , , , , , , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
Texto Completo: | http://www.alice.cnptia.embrapa.br/alice/handle/doc/940202 |
Resumo: | 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. |
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spelling |
A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni.SchistosomaSchistosomiasis 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.ANNA V. PROTASIO, Wellcome Trust Sanger InstituteISHENG J. TSAI, Wellcome Trust Sanger InstituteANNE BABBAGE, Wellcome Trust Sanger InstituteSARAH NICHOL, Wellcome Trust Sanger InstituteMARTIN HUNT, Wellcome Trust Sanger InstituteMARTIN A. ASLETT, Wellcome Trust Sanger InstituteNISHADI DE SILVA, Wellcome Trust Sanger InstituteGILES S. VELARDE, Wellcome Trust Sanger InstituteTIM J. C. ANDERSON, Texas Biomedical Research InstituteRICHARD C. CLARK, Wellcome Trust Sanger InstituteCLAIRE DAVIDSON, Wellcome Trust Sanger InstituteGARY P. DILLON, Wellcome Trust Sanger InstituteNANCY E. HOLROYD, Wellcome Trust Sanger InstitutePHILIP T. LOVERDE, University of Texas Health Science CenterCHRISTINE LLOYD, Wellcome Trust Sanger InstituteJACQUELLINE MCQUILLAN, Wellcome Trust Sanger InstituteGUILHERME OLIVEIRA, Centro de Pesquisas René Rachou, Fundação Oswaldo CruzTHOMAS D. OTTO, Wellcome Trust Sanger InstituteSOPHIA J. PARKER-MANUEL, University of YorkMICHAEL A. QUAIL, Wellcome Trust Sanger InstituteR. ALAN WILSON, University of YorkADHEMAR ZERLOTINI NETO, CNPTIADAVID W. DUNNE, University of CambridgeMATTHEW BERRIMAN, Wellcome Trust Sanger Institute.PROTASIO, A. V.TSAI, I. J.BABBAGE, A.NICHOL, S.HUNT, M.ASLETT, M. A.SILVA, N. deVELARDE, G. S.ANDERSON, T. J. C.CLARK, R. C.DAVIDSON, C.DILLON, G. P.HOLROYD, N. E.LOVERDE, P. T.LLOYD, C.MCQUILLAN, J.OLIVEIRA, G.OTTO, T. D.PARKER-MANUEL, S. J.QUAIL, M. A.WILSON, R. A.ZERLOTINI, A.DUNNE, D. W.BERRIMAN, M.2018-05-11T00:37:25Z2018-05-11T00:37:25Z2012-11-2120122020-04-14T11:11:11Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlePLOS Neglected Tropical Diseases, v. 6, n. 1, p. 1-13, Jan. 2012.http://www.alice.cnptia.embrapa.br/alice/handle/doc/94020210.1371/journal.pntd.0001455enginfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)instacron:EMBRAPA2018-05-11T00:37:31Zoai:www.alice.cnptia.embrapa.br:doc/940202Repositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestopendoar:21542018-05-11T00:37:31falseRepositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestcg-riaa@embrapa.bropendoar:21542018-05-11T00:37:31Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)false |
dc.title.none.fl_str_mv |
A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni. |
title |
A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni. |
spellingShingle |
A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni. PROTASIO, A. V. Schistosoma |
title_short |
A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni. |
title_full |
A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni. |
title_fullStr |
A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni. |
title_full_unstemmed |
A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni. |
title_sort |
A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni. |
author |
PROTASIO, A. V. |
author_facet |
PROTASIO, A. V. TSAI, I. J. BABBAGE, A. NICHOL, S. HUNT, M. ASLETT, M. A. SILVA, N. de VELARDE, G. S. ANDERSON, T. J. C. CLARK, R. C. DAVIDSON, C. DILLON, G. P. HOLROYD, N. E. LOVERDE, P. T. LLOYD, C. MCQUILLAN, J. OLIVEIRA, G. OTTO, T. D. PARKER-MANUEL, S. J. QUAIL, M. A. WILSON, R. A. ZERLOTINI, A. DUNNE, D. W. BERRIMAN, M. |
author_role |
author |
author2 |
TSAI, I. J. BABBAGE, A. NICHOL, S. HUNT, M. ASLETT, M. A. SILVA, N. de VELARDE, G. S. ANDERSON, T. J. C. CLARK, R. C. DAVIDSON, C. DILLON, G. P. HOLROYD, N. E. LOVERDE, P. T. LLOYD, C. MCQUILLAN, J. OLIVEIRA, G. OTTO, T. D. PARKER-MANUEL, S. J. QUAIL, M. A. WILSON, R. A. ZERLOTINI, A. DUNNE, D. W. BERRIMAN, M. |
author2_role |
author author author author author author author author author author author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
ANNA V. PROTASIO, Wellcome Trust Sanger Institute ISHENG J. TSAI, Wellcome Trust Sanger Institute ANNE BABBAGE, Wellcome Trust Sanger Institute SARAH NICHOL, Wellcome Trust Sanger Institute MARTIN HUNT, Wellcome Trust Sanger Institute MARTIN A. ASLETT, Wellcome Trust Sanger Institute NISHADI DE SILVA, Wellcome Trust Sanger Institute GILES S. VELARDE, Wellcome Trust Sanger Institute TIM J. C. ANDERSON, Texas Biomedical Research Institute RICHARD C. CLARK, Wellcome Trust Sanger Institute CLAIRE DAVIDSON, Wellcome Trust Sanger Institute GARY P. DILLON, Wellcome Trust Sanger Institute NANCY E. HOLROYD, Wellcome Trust Sanger Institute PHILIP T. LOVERDE, University of Texas Health Science Center CHRISTINE LLOYD, Wellcome Trust Sanger Institute JACQUELLINE MCQUILLAN, Wellcome Trust Sanger Institute GUILHERME OLIVEIRA, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz THOMAS D. OTTO, Wellcome Trust Sanger Institute SOPHIA J. PARKER-MANUEL, University of York MICHAEL A. QUAIL, Wellcome Trust Sanger Institute R. ALAN WILSON, University of York ADHEMAR ZERLOTINI NETO, CNPTIA DAVID W. DUNNE, University of Cambridge MATTHEW BERRIMAN, Wellcome Trust Sanger Institute. |
dc.contributor.author.fl_str_mv |
PROTASIO, A. V. TSAI, I. J. BABBAGE, A. NICHOL, S. HUNT, M. ASLETT, M. A. SILVA, N. de VELARDE, G. S. ANDERSON, T. J. C. CLARK, R. C. DAVIDSON, C. DILLON, G. P. HOLROYD, N. E. LOVERDE, P. T. LLOYD, C. MCQUILLAN, J. OLIVEIRA, G. OTTO, T. D. PARKER-MANUEL, S. J. QUAIL, M. A. WILSON, R. A. ZERLOTINI, A. DUNNE, D. W. BERRIMAN, M. |
dc.subject.por.fl_str_mv |
Schistosoma |
topic |
Schistosoma |
description |
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. |
publishDate |
2012 |
dc.date.none.fl_str_mv |
2012-11-21 2012 2018-05-11T00:37:25Z 2018-05-11T00:37:25Z 2020-04-14T11:11:11Z |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/publishedVersion info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
PLOS Neglected Tropical Diseases, v. 6, n. 1, p. 1-13, Jan. 2012. http://www.alice.cnptia.embrapa.br/alice/handle/doc/940202 10.1371/journal.pntd.0001455 |
identifier_str_mv |
PLOS Neglected Tropical Diseases, v. 6, n. 1, p. 1-13, Jan. 2012. 10.1371/journal.pntd.0001455 |
url |
http://www.alice.cnptia.embrapa.br/alice/handle/doc/940202 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
reponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa) instacron:EMBRAPA |
instname_str |
Empresa Brasileira de Pesquisa Agropecuária (Embrapa) |
instacron_str |
EMBRAPA |
institution |
EMBRAPA |
reponame_str |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
collection |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
repository.name.fl_str_mv |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa) |
repository.mail.fl_str_mv |
cg-riaa@embrapa.br |
_version_ |
1794503453914955776 |