Schistosoma mansoni Genome Browser

USP - University of São Paulo, Brazil

Schistosoma mansoni Genome Browser is a tool implemented by the A-ParaDDisE (Anti-Parasitic Drug Discovery in Epigenetics) project. This is a project funded by the European Community that employs a target-based strategy for the development of novel drug leads against schistosomiasis, leishmaniasis, Chagas disease and malaria focusing on key histone modifying enzymes (HME), in particular those involved in acetylation/deacetylation and methylation/demethylation.

All data displayed in the browser can be downloaded in BED and FASTA format using the Tools ➝ Table Browser menu.

Project Results

This tool was developed to help the A-ParaDDisE investigators to explore the data and to communicate the results obtained in the context of its Work-Package 3 (WP3): "Functional characterization and target validation", which intends, among other objectives, to obtain Gene Signatures of drug action on parasites. Specifically, in this website we will show the genome-wide mapping of RNA-Seq data obtained with S. mansoni parasites treated with the drugs tested in the project. At present, no public results from A-ParaDDisE WP3 are yet available, and the site shows the public data on S. mansoni gene expression and histone marks.

Restricted Access

If you are a member of the A-ParaDDisE research project you can have early access to the WP3 data on the effect of tested drugs, previous to publication, by sending an e-mail requesting a personal login and password. Please, send e-mail to admin-gene@iq.usp.br.

Additional relevant public S. mansoni databases

WormBase ParaSite: http://parasite.wormbase.org/index.html
Para-site: http://parasite.org.au/para-site/introduction/
SchistoDB: http://schistodb.net/schisto/
GeneDB-schistosoma: http://www.genedb.org/Homepage/Smansoni

Funding

EUROPEAN COMMISSION 7th Framework Programme for Research, Technological Development and Demonstration

"This project has received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no. 602080”

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Please,

Send e-mail to admin-gene@iq.usp.br for any questions and suggestions regarding this assembly hub and its underlying data.

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Restricted access,

If you are a member of the A-ParaDDisE research project you can have early access to the data, previous to publication, by sending an e-mail requesting a personal login and password. Please, send e-mail to admin-gene@iq.usp.br

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Gene Network Public Assembly Hub for Schistosoma mansoni

Credits

• Genome data has been provided by the Welcome Trust Sanger Institute through its FTP site (ftp://ftp.sanger.ac.uk/pub/project/pathogens/Schistosoma/mansoni/).

• This assembly hub was prepared by David da Silva Pires, from Instituto Butantan.

• Webpage prepared by Lucas Ferreira da Silva

• Photo taken by Adriana S. A. Pereira

Please, send e-mail to admin-gene@iq.usp.br for any questions and suggestions regarding this assembly hub and its underlying data.

Genome sequence

This assembly hub contains version 5.2 of the Schistosoma mansoni genome (from A.V. Protasio et al., PLoS Negl Trop Dis 6(1): e1455, 2012). There are 885 chromosomes and scaffolds with sizes from 330 to 65,476,681 nucleotides.

Tracks:

The following tracks (organized by groups) were processed by members of the Laboratory of Gene Expression in Eukaryotes, headed by Sergio Verjovski-Almeida, using public data from the papers indicated below.

Mapping and Sequencing

• Base Position

• Assembly

• Gaps

• GC percent

• Short Match

Genes and Gene Predictions

• MEGs processed by Bruno F. de Souza (R. deMarco et al., Genome Research 20: 1112-1121, 2010; G.T. Almeida et al., Exp. Parasitol. 132: 22-31, 2012).

• SMPs v5.2 processed by Elton J.R. de Vasconcelos (A.V. Protasio et al., PLoS Negl Trop Dis 6(1): e1455, 2012). Schistosoma mansoni gene annotations version 5.2 were downloaded from ftp://ftp.sanger.ac.uk/pub/pathogens/Schistosoma/mansoni/ Latest_assembly_annotation_others/Schistosoma_mansoni_v5.2.gff The bed file provided as track hub was generated by an ad-hoc PERL script. A total of 3,348 SMPs were updated with 5'UTR annotations; 4,068 SMPs were updated with 3'UTR annotations; 639 SMPs presented errors/ambiguity on either their 5'- or 3'UTR annotations. Thus, they were kept as CDS-only exons on the bed file.

mRNA and EST

• 454 male contigs – RNA-Seq data from adult male parasites from G.T. Almeida et al., Exp. Parasitol. 132: 22-31, 2012.

• ESTs from dbEST at NCBI (as of June 2015)

Regulation

• H3K4me3, H3K9ac, H3K9me3, H3K27me3 in cercariae, miracidia, schistosomula and adult worms – ChIP-Seq data processed by Letícia Anderson from the following papers: D. Roquis et al., Front. Genet. 5: 207, 2014; J.M. Lepesant et al., Exp. Parasitol. 135(2): 350-6, 2013; D. Roquis et al., PLoS Negl. Trop. Dis. 9(8): e0003853, 2015. The HOMER ChIP-Seq pipeline (S. Heinz et al., Mol. Cell 38: 576-589, 2010) was applied, finding significant peaks from ChIP-enriched regions.

• CpG Islands processed by Elton J.R. de Vasconcelos. The algorithm developed by Takai & Jones, 2002 (PMID: 11891299) was applied aiming the in silico prediction of CpG islands on S. mansoni genome. The parameters used were the following: GCC = 55%, OE = 0.65 and LENGTH = 200

Repeats

• RepeatMasker (J.M. Lepesant et al., Exp Parasitol. 130(4):470-474, 2012)

Project coordinator:

Prof. Dr. Sergio Verjovski-Almeida (verjo@iq.usp.br)

Department of Biochemistry, Chemistry Institute

University of São Paulo, Brazil