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Notos v 1.0

cpl14

Schistosoma bovis gene prediction :

TrackHub of AUGUSTUS gene prediction


TrackHub of the IHPE for Schistosoma mansoni v5

ChIP-Seq data for the entire life cycle for H3K4me3 and H3K27me3

Schistosoma mansoni repetitive sequences

For assembly version 3.1 (scaffold level):

For assembly version 5.2 (chromosome level):

Please cite:

Lepesant, J.M., Roquis, D., Emans, R., Cosseau, C., Arancibia, N., Mitta, G. and Grunau, C.: Combination of de novo assembly of massive sequencing reads with classical repeat prediction improves identification of repetitive sequences in Schistosoma mansoni. Exp Parasitol (2012) [PubMed] [ScienceDirect]

Female-specific repeats (more than 99% are on W-chromosome):

Please cite:

Lepesant, J.M., Cosseau, C., Boissier, J., Freitag, M., Portela, J., Climent, D., Perrin, C., Zerlotini, A. and Grunau, C.: Chromatin structure changes around satellite repeats on the Schistosoma mansoni female sex chromosome suggest a possible mechanism for sex chromosome emergence. Genome Biol 13 (2012) R14. [PubMed]

Schistosoma mansoni ChIP-Seq data

Reads in Fastq format:

  • SRA study SRP007636 : ChIP-Seq for S.mansoni miracidia, cercaria, adult (male+female)

Please cite:

Cosseau, C. Azzi, A. Smith, K. Freitag, M. Mitta, G. Grunau, C. (2009). Native chromatin immunoprecipitation (N-ChIP) and ChIP-Seq of Schistosoma mansoni: critical experimental parameters. Molecular and Biochemical Parasitology, 166 : 70-76. [PubMed]

Schistosoma mansoni genomic DNA NGS data

Reads in Fastq format:

  • SRA study SRP002052 : genomic NGS for S.mansoni DFO strain, male and female separated

Please cite:

Portela J, Grunau C, Cosseau C, Beltran S, Dantec C et al. (2010) Whole-genome in-silico subtractive hybridization (WISH) – using massive sequencing for the identification of unique and repetitive sex-specific sequences: the example of Schistosoma mansoni. BMC Genomics 11: 387. [PubMed]

Schistosoma mansoni adult male and female transcriptome after treatment of cercariae with latex

[download link]

Please cite:
Augusto R et al. Double impact: natural molluscicide for schistosomiasis vector control also impedes development of Schistosoma mansoni cercariae into adult parasites” (Plos NTD 2017)

Schistosoma mansoni sex specific transcriptome

Total RNA was extracted from male and female cercariae, schistosomula and adults. Schistosoma mansoni SmGH2 was used and maintained in Biomphalaria glabrata snail, strain BgGua and Swiss OF1 mice. In order to obtain unisexual clones of cercariae, monomiracidial infections of mollusks were performed. In vivo unisexual schistosomula were obtained by perfusions of the hepatic portal system between three and four weeks post-infection (PI) and were sorted into three finely defined stages (s#1, s#2 and s#3, from the younger to the older). Sorting criteria are based on caecum shape, acetabulum location and gynaecophoric canal appearance in males. Male and female adult worms were recovered from the unisexually infected mice after 49 days PI by perfusion.

                                                                                                                                                                 

bg

Biomphalaria glabrata reference transcriptome

Contigs in Fasta format:

Reference transcriptome : Total RNA was extracted from 2 pools of 30 individuals of B glabrata isolated from Brazil (BgBRE). Each pool was constituted from 10 juveniles, 10 adults and 10 senescent individuals. The transcriptome of B. glabrata was assembled de novo from 157 million of high quality trimmed paired-end 72 bp reads obtained by Illumina sequencing. We have performed a multiple k-mers assembly approach using Velvet and Oases. The obtained transcriptome consists of 117,269 transcripts of more than 100 bp.

Please cite

Dheilly NM, Duval D, Mouahid G, Emans R, Allienne JF, Genthon C, Dubois E, Du Pasquier L, Adema C, Grunau C, Mitta G, and Gourbal B. De novo assembly of transcriptome from RNA-seq data as a tool to reveal the complexity of the snail Biomphalaria glabrata immune system. Release date: 2013

                                                                                                                                                                 




Pseudosuccinea columella reference transcriptome

Vector snail of Fasciola hepatica in Cuba.

A de novo transcriptome of P. columella was assembled using high-quality reads (quality > 38 phred score) from six sequenced samples using the default options of Trinity 2.0.6.1 method (Grabher et al., 2011) on the Galaxy Project server (Giardine et al., 2005). From a total of 592 million raw reads, the first consensus transcriptome for P. columella resulted into 158 837 contigs. To reduce its complexity, Trinity Super Assembly (Grabher et al., 2011) was applied to the de novo assembled transcriptome, and all transcripts shorter than 300 pb were removed, with 78 774 transcripts remaining for further analysis. Afterwards, we reduce hypervariable families by CD-Hit-est (Li and Godzik, 2006) to cluster transcripts with matches above 95% identity, resulting in 72 748 transcripts.

Fichier fasta : Pcol-CD-HIT-EST95_Transcriptome_300.fasta

                                                                                                                                                                   

pdarmi

Pocillopora damicornis reference transcriptome

Contigs in Fasta format:

  • Reference transcriptome: RNA-seq read de novo assembled (Velvet plus Oases plus TIGR) from adult P. damicornis (one clone only) exposed to acidification treatments (3 weeks at pH7.4 and 3 weeks at pH 8.3), thermal stress (Vidal-Dupiol et al. 2009 BMC Physiology), bacterial stress (Vidal-Dupiol et al. 2011 J Exp Biol), bacterial infection (Vidal-Dupiol et al. 2011 J Exp Biol) and control treatment.

Please cite

Vidal-Dupiol J., Zoccola D., Tambutte E., Grunau C., Cosseau C., Smith K.M., Freitag M., Adjeroud   M., Dheilly N.M., Allemand  D., Mitta G. & Tambutte S. (under 2dn review). Whole-transcriptome analysis of a reef-building coral exposed to CO2-driven pH decrease reveals upregulation of ion transport, organic matrix proteins and energy requirement at the transcriptomic level: a way to cope with ocean acidification? PlosOne, Release date: 2013

Pocillopora damicornis RNA-seq data

Reads in Fastq format:

  • SRA study SRP011059.1: RNA-seq for adult P. damicornis (one clone only) exposed to acidification. Treatments: 3 weeks at pH7.4 and 3 weeks at pH 8.3

Please cite

Vidal-Dupiol J., Zoccola D., Tambutte E., Grunau C., Cosseau C., Smith K.M., Freitag M., Adjeroud   M., Dheilly N.M., Allemand  D., Mitta G. & Tambutte S. (under 2dn review). Whole-transcriptome analysis of a reef-building coral exposed to CO2-driven pH decrease reveals upregulation of ion transport, organic matrix proteins and energy requirement at the transcriptomic level: a way to cope with ocean acidification? PlosOne, Release date: 2013.

Reads in Fastq format:

SRA study : SRP029998 : RNA-seq for adult P. damicornis exposed to non virulent bacteria, virulent bacteria and thermal stress.

Please cite

Jeremie Vidal-Dupiol, Nolwenn M Dheilly, Rodolpho Rondon, Christoph Grunau, Celine Cosseau, Kristina Smith, Michael Freitag, Mehdi Adjeroud, Guillaume Mitta(submitted). Deeper inside the coral diseases puzzle: high temperature lead to transcriptome remodeling favorable for infection, while virulent bacteria induce immuno-suppression.

                                                                                                                                                                  

cocc

 

Coleomegilla maculata reference transcriptome

Dinocampus coccinellae reference transcriptome

Contigs in Fasta format:

For the host total RNA was extracted from heads and abdomens of healthy and infected ladybirds (Coleomegilla maculate). For the parasite the wasp Dinocampus coccinellae total RNA was extracted from larvae collected before egression and after egression. RNA from 12 individuals was pooled for each experimental conditions and paired-end sequencing was performed with Illumina. A transcriptome was assembled de novo for each sample. Then, we used Cd-hit-est to generate the reference transcriptomes. The first transcriptome represented the transcriptome of healthy and infected ladybird. The second transcriptome represented the transcriptome of the wasp D. coccinellae larvae collected before and after egression.

Reference transcriptome of Coleomegilla maculata
Reference transcriptome of Dinocampus coccinelae

Please cite

Dheilly NM, Maure F, Ravallec M, Doyon J, Galinier R, Duval D, Volkoff N, Brodeur J, Gourbal B, Mitta G, Thomas F. Who’s the puppet master? A virus mediates the bodyguard behavior by a parasitic wasp. Release date: 2013