Genomes we don’t have in WormBase ParaSite

The work on the version 11 of WormBase ParaSite is ongoing! We now have a list of assemblies of new species, and improved genomes of existing species, that we plan to publish. As well as including data submitted to us directly, we also surveyed the archives and have made an effort to include all assemblies of taxa Nematoda and Platyhelminthes  available in NCBI and ENA that have been annotated with gene structures.

We seem to be doing well in our attempts to reflect the sequencing efforts of relatives of Caenorhabdhitis elegans – the order Rhabditida makes up 43 of our 100 Nematoda genomes. This good coverage seems to extend to other nematodes relevant to answering basic biology questions, for nematodes causing disease in humans and livestock, and for parasites of plants.

The situation is very different for our other phylum of interest, Platyhelminthes, which is more diverse, and has historically been harder to study due to complex life cycles of these animals. There isn’t a clear model organism like C. elegans for Nematoda for parasitologists to use to study Platyhelminthes, but many species, like the flukes F. hepatica and S. mansoni, are subject to active research.

In particular, phylum Platyhelminthes has a class Turbellaria of free-living marine worms, full of ancient, evolutionarily unique and remarkable organisms, like this Pseudobiceros bedfordi : a large colorful flatworm that feeds on ascidians and small crustaceans.

 

Some species of this class are studied due to their unusual properties. We are tracking research in the area, and currently have two genomes of Turbellaria – Macrostomum lignano and Schmidtea mediterranea.

M.lignano is a tiny worm living in shore sands of Adriatic sea, and is used as a model organism for a number of evolutionary studies. We’ll be publishing an update to this genome, sequenced in 2017 by University Medical Center Groningen.

S. mediterranea is a freshwater species, important for research in stem cells and regeneration. ParaSite currently hosts the original published version of the Schmidtea genome, from 2014. Another group has since published  a new and improved assembly. We are hopeful that the authors will annotate this version of the genome with gene structures soon, so that we can include it in ParaSite.

Do reach out to us if you have a potential submission, know of a published genome that could be included in ParaSite, or to tell us about ongoing research about Nematoda or Platyhelminthes that should be on our radar.

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3 thoughts on “Genomes we don’t have in WormBase ParaSite”

  1. Is there any possibility of getting the genome of Pratylenchus coffeae into ParaSite? It was published in 2015 (https://doi.org/10.1163/15685411-00002901), and is a remarkable genome (19.7 Mb with 6,712 protein-coding genes — one of the smallest for a metazoan), but has been unobtainable on any public database.

    It should be possible to obtain the genome sequence with its annotation data from Charles Opperman at https://plantpath.cals.ncsu.edu/people/faculty/charles-opperman. The raw sequencing reads are available at http://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA276478, although the genome seems not to have been deposited anywhere yet.

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    1. It’s on our radar! I have talked to prof. Blaxter at a conference in Hinxton, they have the genome and will reannotate it. It will probably appear on caenorhabditis.org a little earlier, and we’ll get the genomes through the archives.

      The comment also featured prof. Opperman’s email – I’ve removed it from the comment, WordPress is terrible for spam.

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