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 for biologists to study due to complex life cycles of these animals. The phylum doesn’t have a clear model organism like C. elegans, 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 TurbellariaMacrostomum 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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Announcing WormBase ParaSite 10

We are pleased to announce the tenth release of WormBase ParaSite. We have included genomes of four new species, bringing the total number of genomes to 138, representing 118 distinct species, and updated the assemblies or annotations of an additional four. This includes results of recent efforts to sequence Ascaridae genomes (Wang et al, 2017): a much improved assembly of Ascaris suum, with an N50 of 4.6Mb up from 290.6kb, and a newly sequenced Parascaris univalens. The other three new genomes are of particular interest to the study of nematode reproduction. These are two species of the genus Diploscapter, D. coronatus (Hiraki et al, 2017) and D. pachys (Fradin et al, 2017), which have managed to stay adaptable and maintain genetic variation throughout their long evolutionary history as parasites; and the free-living Caenorhabditis nigoni (Yin et al, 2018), a parthenogenic cousin of hermaphroditic C. briggsae.

The assembly and annotation of Echinococcus canadensis are now in line with the paper introducing the genome (Maldonado et al, 2017). We also have included a tidy-up update of the assembly of Schistosoma haematobium. For the WormBase core species, we have updated the annotations to WS263. As with each release, we have updated our comparative genomics data – recalculating the orthologues and paralogues for all species – and the protein features pipeline, annotating genes with protein domains and inferred GO terms using the latest version InterProScan.

What would you like to learn about in our BSP workshop?

We’re looking forward to presenting a workshop at the upcoming BSP Spring meeting in Aberystwyth. To help us prepare, we’d love to know what our users would find most useful for us to cover. Please fill in our quick survey (one question only!): https://www.surveymonkey.co.uk/r/8LYF2YW

 

Announcing WormBase ParaSite Release 9

We are pleased to announce the ninth release of WormBase ParaSite.  In this release, we have included genomes for two new species (Ditylenchus destructor – PRJNA312427 and Taenia saginata – PRJNA71493) and an additional alternative genome for one species (Taenia asiatica – PRJNA299871).  This brings the total number of genomes to 134, representing 114 species.  Additionally, all WormBase core species have been updated to release WS258.

As part of this release, we have introduced a new genome browser: JBrowse (example for S. mansoni).  This offers a fast and interactive experience for all genomes.  Custom tracks can be attached directly from a local computer, without needing to upload any data.  This makes JBrowse ideal for visualising large data files, without the need to download or install any additional software.  Other features include combination tracks for visualising multiple files as a single track, and sequence search tracks for locating short sequence motifs within the genome.

Featured paper: The Echinococcus canadensis (G7) Genome

Tapeworms of the Echinococcus granulosus sensu lato species complex cause the zoonotic disease echinococcosis. Maldonado et al, from the Kamenetzky group at the University of Buenos Aires, have recently reported the genome assembly and annotation of one of the members of this species complex, Echinococcus canadensis (G7 genotype). The genome paper additionally describes a number of comparative analyses between E. canadensis (G7), E. canadensis (G1) and E. multilocularis, based on gene orthology, genome-wide SNP analyses and identification of regulatory features.

Version 1 of the E. canadensis (G7) genome is currently available in WormBase ParaSite, with version 2 becoming available in release 10.

Travel bursaries announced for Hydra conference

Up to 3 awards will be made for early-career researchers from Africa, Asia and Latin America to support participation at the meeting; the bursaries will cover registration fees (GBP 495, approx USD 625), and a sum of USD 1000 towards airfare and ground transportation costs. Awardees will be selected on the basis of Abstracts submitted to the conference, and a letter of application outlining the reasons for attending the meeting. Applicants should register through this website and send their application letter to Hydra@ed.ac.uk before the closing date of 31 March 2017.

Conference website: http://hydra.bio.ed.ac.uk/

 

Registration open for BSP Spring Meeting 2017

Registration is now open for the British Society for Parasitology Spring Meeting, to be held in Dundee from 2nd April to 5th April 2017.

WormBase ParaSite will be present throughout the conference, including a workshop session.  We will also be available to answer questions and provide practical demonstrations.  More details will follow.

Abstract submission deadlines:
Oral presentation – 19th February 2017
Poster – 5th March 2017

More details and registration for the conference: http://bsp.uk.net/2016/10/04/bsp-spring-meeting-2017/

We look forward to seeing you in Dundee!