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.

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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.

Parasitic Nematodes: Bridging the Divide workshop abstract solicitation

As part of the 21st International C.elegans conference, we would like to solicit contributions to the workshop on parasitic nematodes.

We are pleased to invite student and postdoc abstract submissions for 5 minute lightning talks to be presented at the NSF-sponsored, 3rd Parasitic Nematodes: Bridging the Divide workshop. We encourage submissions that address the broad theme of C. elegans as a model for parasitic nematode biology, including work relating to human, animal, and plant parasitic nematodes and from both a basic biology standpoint or a translational perspective. The platform provided by this workshop represents a unique opportunity for early-career scientists to interact with other researchers at the intersection of C. elegans biology and parasitology. These five minute talks will be presented on the first day of the 21st International C. elegans Meeting. The presenting authors must be available during any of the limited number of possible time slots available. Abstract submissions are due on May 12th at 5pm PST and presenting authors will be notified of decisions by May 19th. Instructions for logistics and formatting of lightning talk presentations will follow acceptance.

Abstract Format: Abstracts should be limited to 2,500 characters in total, including the title, authors, author affiliations, main body, and spaces. Abstracts should be sent to the workshop e-mail address (parasiteworkshop@gmail.com) as a single PDF file with subject heading “Lightning Talk Abstract”. A notification of receipt will follow submission. Accepted abstracts will appear online in a Worm Breeder’s Gazette article and titles will be listed on the International Worm Meeting website.

Workshop Date: Wednesday, June 21, 2017
Workshop Time: 2:30pm- 5:30pm
Workshop Location: Sunset Village Grand Horizon Ballroom

Lightning Talk Abstract Submission Deadline: May 12, 2017 (5pm PST)
Notification of Acceptance: May 19, 2017

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!