title: A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni.
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.
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom.
authors.forename: Anna V
authors.initials: AV
authors.lastname: Protasio
authors.forename: Isheng J
authors.initials: IJ
authors.lastname: Tsai
authors.forename: Anne
authors.initials: A
authors.lastname: Babbage
authors.forename: Sarah
authors.initials: S
authors.lastname: Nichol
authors.forename: Martin
authors.initials: M
authors.lastname: Hunt
authors.forename: Martin A
authors.initials: MA
authors.lastname: Aslett
authors.forename: Nishadi
authors.initials: N
authors.lastname: De Silva
authors.forename: Giles S
authors.initials: GS
authors.lastname: Velarde
authors.forename: Tim J C
authors.initials: TJ
authors.lastname: Anderson
authors.forename: Richard C
authors.initials: RC
authors.lastname: Clark
authors.forename: Claire
authors.initials: C
authors.lastname: Davidson
authors.forename: Gary P
authors.initials: GP
authors.lastname: Dillon
authors.forename: Nancy E
authors.initials: NE
authors.lastname: Holroyd
authors.forename: Philip T
authors.initials: PT
authors.lastname: LoVerde
authors.forename: Christine
authors.initials: C
authors.lastname: Lloyd
authors.forename: Jacquelline
authors.initials: J
authors.lastname: McQuillan
authors.forename: Guilherme
authors.initials: G
authors.lastname: Oliveira
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Otto
authors.forename: Sophia J
authors.initials: SJ
authors.lastname: Parker-Manuel
authors.forename: Michael A
authors.initials: MA
authors.lastname: Quail
authors.forename: R Alan
authors.initials: RA
authors.lastname: Wilson
authors.forename: Adhemar
authors.initials: A
authors.lastname: Zerlotini
authors.forename: David W
authors.initials: DW
authors.lastname: Dunne
authors.forename: Matthew
authors.initials: M
authors.lastname: Berriman
mesh_terms: D000818:Animals; D018509:DNA, Helminth / Q000737:chemistry / Q000235:genetics; D049751:Genome, Helminth; D008969:Molecular Sequence Data; D018510:RNA, Helminth / Q000235:genetics; D012550:Schistosoma mansoni / Q000235:genetics*; D017422:Sequence Analysis, DNA; D059467:Transcriptome
chemical_list: D018509:DNA, Helminth; D018510:RNA, Helminth