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Data released on May 19, 2016

Resource for “Transcriptome sequences spanning key developmental states as a resource for the study of the cestode Schistocephalus solidus, a threespine stickleback parasite.”

Aubin-Horth, N; Barber, I; Grambauer, S; Hebert, F, O; Landry, C, R (2016): Resource for “Transcriptome sequences spanning key developmental states as a resource for the study of the cestode Schistocephalus solidus, a threespine stickleback parasite.” GigaScience Database. http://dx.doi.org/10.5524/100197 RIS BibTeX Text

The cestode Schistocephalus solidus has been the focus of extensive research in parasitology for over 200 years and has now become a powerful model for studying host-parasite interactions. S. solidus can be utilized to better understand the complex molecular mechanisms underlying functional changes associated with host transitions. We have sequenced and assembled (de novo) the transcriptome of S. solidus using whole organisms from three key developmental stages involved in host transitions: immature plerocercoid, mature plerocercoid and adult. Recent publications in parasitology, and more specifically on host-parasite interactions, have been strongly focused towards reviews and development of ideas and theoretical frameworks, but empirical data acquisition is still lagging behind. The main objective underlying the publication of this data is to increase the amount of publicly available resources for host-parasite systems.
Our de novo assembly pipeline for the transcriptome of Schistocephalus solidus allowed us to reconstruct 24,765 high-confidence, non-redundant transcripts, associated with 10,285 unique genes. In total 7,323 unique genes (71%) were assigned at least one gene ontology (GO) term, and 4,270 (35%) were assigned at least one KEGG pathway ID. Phylogenetic relationships with other parasitic and non-parasitic worm species were investigated, allowing the identification of 1,977 genes that are specific to S. solidus, 3,425 core orthologs shared only among parasites and 6,892 putative orthologs shared among all worm species included in the analysis.
Accessibility to high-quality genetic resources for a wide panel of host-parasite systems is fundamental not only to the advancement of knowledge on the mechanisms of host-parasite interactions, but also on the evolution of complex life cycles and parasitism itself. This is, to our knowledge, the first large-scale transcriptomic dataset for Schistocephalus solidus.

Contact Submitter

Related manuscripts:

doi:10.1186/s13742-016-0128-3

Protocols.io:

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Keywords:

transcriptome flatworm host-parasite stickleback RNA-seq 

Transcriptomic

http://gigadb.org/images/data/cropped/100197_ssol.jpg

Funding:

  • Funding body - Fonds de Recherche du Québec Nature et Technologies
  • Award ID - equipe
  • Comment - Nadia Aubin-Horth
  • Funding body - Fonds de Recherche du Québec Nature et Technologies
  • Award ID - equipe
  • Comment - Christian Landry
  • Funding body - Natural Sciences and Engineering Research Council of Canada
  • Award ID - Discovery
  • Comment - Nadia Aubin-Horth
  • Funding body - Natural Sciences and Engineering Research Council of Canada
  • Award ID - VANIER
  • Comment - Francois Olivier Hebert

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Ssol.cltw.A.0370667  Schistocephalus solidus Description:short PE reads
Tissue:whole organism
Life stage:adult
...
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Ssol.cltw.A.0770667  Schistocephalus solidus Description:short PE reads
Tissue:whole organism
Life stage:adult
...
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Ssol.cltw.A.1270667  Schistocephalus solidus Description:long PE reads
Tissue:whole organism
Life stage:adult
...
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Ssol.cltw.I.0170667  Schistocephalus solidus Description:short PE reads
Tissue:whole organism
Life stage:adult
...
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Ssol.cltw.I.6370667  Schistocephalus solidus Description:short PE reads
Tissue:whole organism
Life stage:mature plerocercoid
...
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Ssol.cltw.I.6770667  Schistocephalus solidus Description:short PE reads
Tissue:whole organism
Life stage:mature plerocercoid
...
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Ssol.cltw.I.98.170667  Schistocephalus solidus Description:short PE reads
Tissue:whole organism
Life stage:mature plerocercoid
...
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Ssol.cltw.I.98.270667  Schistocephalus solidus Description:short PE reads
Tissue:whole organism
Life stage:mature plerocercoid
...
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Ssol.cltw.NI.0570667  Schistocephalus solidus Description:short PE reads
Tissue:whole organism
Life stage:immature plerocercoid
...
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Ssol.cltw.NI.0870667  Schistocephalus solidus Description:short PE reads
Tissue:whole organism
Life stage:immature plerocercoid
...
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Displaying 1-10 of 15 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
tabular dataTEXT3.6 MB2016-05-04
tabular dataTEXT8.68 MB2016-05-04
tabular dataTEXT8.69 MB2016-05-04
transcriptome sequenceFASTA191.54 MB2016-05-04
ReadmeTEXT3.1 KB2016-05-04
tabular dataCSV7.56 KB2016-05-04
tabular dataCSV6 KB2016-05-04
Ssol.cltw.NI.05imageBMP422.35 KB2016-05-04
Ssol.cltw.NI.08imageBMP422.35 KB2016-05-04
Ssol.cltw.NI.12imageBMP422.35 KB2016-05-04
Displaying 1-10 of 27 File(s).

History:

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