About archive sites

We’re pleased to announce that we have introduced an archiving service.

From release 16 onwards, older WormBase ParaSite releases will remain available for browsing. We have introduced this service to help users in transitions between genome and annotation versions. Older, draft assemblies are increasingly being superseded by highly contiguous assemblies generated with modern sequencing technologies. We want to host this data where it is available, but recognise that direct replacement of older assembly versions can cause disruption to researchers.

In release 16, we have updated gene models for 12 assemblies and replaced one assembly, Clonorchis sinensis (PRJNA386618), with a more highly scaffolded version. All superseded data remains available on the release 15 archive site:

https://release-15.parasite.wormbase.org/index.html

Due to technical restrictions, the site has slightly reduced functionality compared with the live site. BLAST and VEP tools are not available. BioMart does remain available.

The search service is also not available. To navigate to a gene page, paste its ID directly into the URL. For example:

https://release-15.parasite.wormbase.org/Gene/Summary?g=maxplancki-mkr-S2-19.22-mRNA-1

Where “maxplancki-mkr-S2-19.22-mRNA-1” is a gene stable ID. For annotation updates, deprecated gene pages can also be accessed from the JBrowse genome browser on the live site:

In addition to the archive site, data from all previous releases remains available to download from our FTP site in perpetuity.

Announcing WormBase ParaSite Release 16

We are delighted to announce the 16th release of WormBase ParaSite. Highlights of this release include:

  • Addition of six new genome assemblies
  • Annotation updates for 12 genomes
  • Addition of phenotype data for C. elegans genes, imported from WormBase
  • Addition of gene name synonyms for a set of Strongyloides stercoralis genes
  • Introduction of an archiving service
  • Deprecation of CEGMA, and introduction of BUSCO as an annotation quality metric
  • New repeat feature libraries for all genomes, generated with RepeatModeler2.
New genomes

This release sees the addition of 6 new assemblies, of which 2 are new species:

  • Atriophallophorus winterbourni (new species) – a digenean trematode parasite native to the lakes of New Zealand (from Zajac et al., 2021).
  • Bursaphelenchus okinawaensis (new species) – a lab model for the root knot nematode Bursaphelenchus xylophilus (from Sun et al., 2020).
  • Bursaphelenchus xylophilus – a new chromosome-scale assembly from Dayi et al., 2020.
  • Caenorhabditis remanei – a new chromosome-scale assembly from Teterina et al., 2020.
  • Clonorchis sinensis – a new chromosome-scale assembly from Young et al., 2021.
  • Oscheius tipulae – a new chromosome-scale assembly from Gonzalez de la Rosa et al., 2021.
Annotation updates

We present full annotation updates for a set of genomes:

  • Pristionchus arcanus
  • Pristionchus entomophagus
  • Pristionchus exspectatus
  • Pristionchus fissidentatus
  • Pristionchus japonicus
  • Pristionchus maxplancki
  • Pristionchus mayeri
  • Parapristionchus giblindavisi
  • Micoletzkya japonica

Three further genomes have seen manual gene model curation by the community:

  • Dirofilaria immitis
  • Haemonchus contortus (PRJEB506)
  • Strongyloides stercoralis

For these species, gene models that have been manually verified/curated can be identified with a note in the “Annotation Method” line on their gene page, for example:

For all 12 species with annotation updates, previous gene models can be visualised in JBrowse in the “WBPS15 gene models track”:

Deprecated gene models and assemblies (and associated analyses) also remain accessible on our new archive site. See this blog post for further information on how to access archived data.

Phenotype data

This release sees the import of over 350,000 C. elegans gene-phenotype associations from our sister site, WormBase. These associations have been curated from the literature over many years, from RNAi and variant data. The data is accessible on C. elegans gene pages:

As the majority of helminth genes don’t currently have data from direct phenotypic assays, phenotypes have also been propagated between orthologues. In the example below, we can see the phenotypes associated with the C. elegans orthologues of a H. polygyrus gene:

In total, we now host phenotype data from 13,350 studies (of which 13,349 C. elegans and 1 Schistosoma mansoni).

Gene name synonyms

We have imported 375 gene name synonyms for Strongyloides stercoralis. These gene names have been curated from the literature by Jonathan Stoltzfus of Millersville University; we hope that storing these synonyms will improve discoverability and connectivity to the literature. The synonyms are searchable, and where present appear in the new “Synonyms” line of the gene page:

We can now see papers referring to this gene in the literature tab:

Many thanks to Jonathan Stoltzfus for providing this data!

deprecation of cegma and BUSCO update

In recognition of the fact that CEGMA has not been supported for several years, we have deprecated CEGMA scores for WormBase ParaSite assemblies. Instead, we now report two BUSCO metrics: one based on the genome assembly and another on the annotation. See the BUSCO manual for further information on these different modes and on interpreting BUSCO scores.

Repeat feature update

We have run RepeatModeler2 to generate custom transposable element (TE) sequence models for all assemblies. The TE sequence files are available to download from our FTP site (repeat-families.fa.gz files):

These custom TE models have also been used for masking, and are available as tracks on the genome browsers. Many thanks to Sanger Institute apprentice Charles Nunn for generating this data.

misc
  • Updated protein domain annotation (InterProScan v. 5.51-85.0), functional annotation and cross referencing for all genomes.
  • Gene identifiers have been mapped between WormBase ParaSite versions for all Pristionchus sp. updates using Ensembl’s mapping method. Where mapped, previous gene IDs are available in GFF downloads and on gene pages.
  • Recomputed orthologues, paralogues and protein families (Ensembl Compara v. 101). Where multiple assemblies exist for the same species, we have only used one assembly for orthology calculations. This means that some assemblies now do not have orthologue and parologue data.

Announcing WormBase ParaSite Release 15

We’re delighted to announce the release of WormBase ParaSite 15, our biggest release yet!

New genomes

This release sees the addition of assemblies of 19 new species:

Genome and annotation updates

We have also incorporated alternative or updated assemblies/gene models for a further 8 species:

  • An alternative (PacBio) assembly from Sun-Yat Sen University for Angiostrongylus cantonensis (PRJNA350391,  Xu et al, 2019).
  • An alternative Hymenolepis diminuta assembly from The University of Warmia and Mazury (PRJEB30942, Nowak et al., 2019).
  • An alternative (PacBio) Steinernema feltiae assembly (PRJNA353610, Fu et al., 2020).
  • An alternative (PacBio) Schistosoma japonicum assembly from Fudan University (PRJNA520774, Luo et al., 2019).
  • Schistosoma haematobium (PRJNA78265) has been updated to reflect an assembly update in INSDC (GCA_000699445.2, Stroehlein et al., 2019). Gene ID mappings from the previous assembly (GCA_000699445.1) are available in the GFF file, and on gene pages.
  • A handful of curated gene models have been added to the Fasciola hepatica (PRJEB25283) annotation, submitted by Emily Robb of Queens’ University Belfast.
  • Curated gene models for the P-glycoprotein repertoire have been added to the Parascaris univalens (PRJNA386823) annotation, submitted by Alexander Gerhard of The Free University of Berlin.
  • The Haemonchus contortus (PRJEB506) annotation has been updated to reflect ongoing curation by Steve Doyle and colleagues at the Wellcome Sanger Institute.

RNAi data

We have imported phenotype data from the recent Schistosoma mansoni RNAi screen by Wang et al., 2020. You can browse the data from S. mansoni gene pages (see the “phenotype” link in the left hand menu). Please let us know if you have any feedback or suggestions for other RNAi studies that you’d like to see in WormBase ParaSite.

Other changes to note

  • The Ancylostoma ceylanicum (PRJNA72583) annotation has been updated to incorporate some missing gene models.
  • Caenorhabditis sp. 34 has been renamed to Caenorhabditis inopinata.
  • In response to feedback from the community, we now present two alternative Steinernema carpocapsae assemblies: GCA_000757645.1, as described by Dillman et al., 2015 and GCA_000757645.3, as described by  Serra et al. (2019). The Serra annotation has been updated to incorporate UTRs, which were omitted in WormBase ParaSite 14. IDs for genes on the X chromosome have also been updated to follow the naming convention of the rest of the gene set. ID mappings between WBPS14 GCA_000757645.3 and WBPS15 GCA_000757645.3 are available on gene pages and in the GFF file. A mapping between gene IDs in GCA_000757645.1 and GCA_000757645.3 is available on the WBPS FTP site.
  • IsoSeq data for the heartworm Dirofilaria immitis is available on JBrowse, submitted by Nic Wheeler and colleagues of the University of Wisconsin-Madison.
  • We have added the alternative Necator americanus gene set, described by Logan et al., 2020, as a JBrowse track.

Alternative gene set for Necator americanus

Logan et al. (2020) have published an alternative set of gene predictions for Necator americanus in PLoS Neglected Tropical Diseases, based on both RNA-seq and proteomics data and generated via the MAKER pipeline.

Their gene predictions can be downloaded from the WormBase ParaSite FTP site at:
ftp://ftp.ebi.ac.uk/pub/databases/wormbase/parasite/datasets/logan_2020_32453752

Thanks to Javier Sotillo Gallego for providing the data!

Parasitic Helminths: New Perspectives in Biology and Infection

30th August – 4th September, 2020: Bratsera Hotel, Hydra, Greece.

Registration: 14 January – 28 February 2020

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

The 14th conference in a series previously titled Molecular and Cellular Biology of Helminth Parasites

About the Meeting

The study of helminth parasites continues to excite great interest across the suite of modern scientific themes. With a wealth of genome information and high-throughput technologies, new drug and vaccine development, and intricate host-parasite molecular interactions, we are witnessing a new era of research on these organisms and the diseases they cause. Parasitic Helminths : New Perspectives in Biology and Infection continues the highly successful series now held every year on the beautiful island of Hydra, Greece. All major helminth research areas are covered, including new genomics of animal- and plant-parasitic nematodes, interfaces with free-living helminths such as C. elegans and planarians, developmental and molecular biology, genetics, neurobiology, pharmacology, immunology and vaccine research, all aimed at creating new strategies for control of these prevalent parasitic organisms and the diseases they cause.

Venue

A key feature of the Hydra venue is the Bratsera Hotel hosting the scientific sessions, and the quiet, traffic-free town with ample facilities for informal interactions between delegates. A wide range of accommodation is available close by, including pensions for those on a tight budget. Attendance is limited to 100 people, consistent with a discussion-orientated meeting in which every delegate is an active participant – early registration is encouraged!

Invited Speakers 2020

Keynote Speaker: Jonathan Ewbank, Marseille, France

Confirmed Speakers:

  • Julie Ahringer, Cambridge, UK
  • Adler Dillman, Riverside, USA
  • Sebastian Eves-van den Akker, Cambridge
  • Jennifer Keiser, Basel, Switzerland
  • Frédéric Landmann, Montpellier, France
  • Meera Nair, Riverside, USA
  • Phil Newmark, Madison, USA
  • Meta Roestenberg, Leiden, Netherlands
  • Mark Siracusa, Newark, USA

Organising Committee

  • Amy Buck, University of Edinburgh
  • James Collins, University of Texas
  • Richard E Davis, University of Colorado
  • Kleoniki Gounaris, Imperial College
  • Rick Maizels, University of Glasgow
  • Murray Selkirk, Imperial College

Brugia pahangi material available

The Devaney group have small numbers of adult B. pahangi and larger numbers of Mf available to others for research purposes.  If this would be useful, please contact eileen.devaney@glasgow.ac.uk with approximate numbers, life stage required and whether fresh or frozen material is suitable. The B. pahangi life cycle is funded by a grant from the Wellcome Trust (208390/Z/17/Z).

Helminth Bioinformatics Course in Accra, Ghana: Open for Applications

We’re pleased to announce that a new Wellcome Advanced Course in helminth bioinformatics is now open for applications. The course is aimed at Africa-based researchers at various levels. It will be a hands on and practical introduction to bioinformatics for helminth researchers, covering:

  • The use of public databases (including WormBase ParaSite) to explore gene and protein function
  • Genome assembly
  • Variant calling
  • Differential gene expression
  • Unix/linux command-line and some basic R

Dates and Deadlines

The course will be held at the West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Accra, Ghana, from 8 -13th September 2019.

The course is free to attend for non-commercial applicants, and a number of bursaries are available to cover travel, accommodation and sustenance.

The deadline for applications is 9th May.

More details are available here: https://coursesandconferences.wellcomegenomecampus.org/our-events/helminth-bioinformatics-ghana-2019/

 

 

Parasitic Helminths: New Perspectives in Biology and Infection

1st – 6th September, 2019: Hydra, Greece.

Registration: 13th Jan- 29th March 2019.

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

 

Title

 

About the meeting

The study of helminth parasites continues to excite great interest across the suite of modern scientific themes. With a wealth of genome information and high-throughput technologies, new drug and vaccine development, and intricate host-parasite molecular interactions, we are witnessing a new era of research on these organisms and the diseases they cause. Parasitic Helminths: New Perspectives in Biology and Infection will be the 13th in a highly successful series now held every year on the beautiful island of Hydra, Greece. All major helminth research areas are covered, including new genomics of animal- and plant-parasitic nematodes, interfaces with free-living helminths such as C. elegans and planarians, developmental and molecular biology, genetics, neurobiology, pharmacology, immunology and vaccine research, all aimed at creating new strategies for control of these prevalent parasitic organisms and the diseases they cause.

 

Meeting home

Meeting registration

Registration for 2019 will open on Monday January 14 and close on Friday March 29. For questions, please email us at hydra@ed.ac.uk
Attendance is limited to 100 people, consistent with a discussion-orientated meeting in which every delegate is an active participant – early registration is encouraged.

Invited speakers 2019

Keynote Speaker

Alejandro Sánchez Alvarado, USA
Small RNA Mini-Symposium

Confirmed Speakers

Amy Buck, Edinburgh, UK
Louisa Cochella, Vienna, Austria
Alison Elliott, Entebbe, Uganda
Carolina Escobar, Toledo, Spain
Elodie Ghedin, New York, USA
Nicola Harris, Melbourne, Australia
Karl Hoffmann, Aberystwyth UK
P’ng Loke, New York USA
Peter Sarkies, London, UK
William Sullivan, Santa Cruz, USA

Example program (2018)

The Meeting Program is organized primarily from abstracts submitted by participants, a small group of invited speakers, and an invited Keynote Speaker. Many abstracts are selected for short talks and there are two poster sessions. Ample time to interact with participants is available with free time in the afternoons to explore the island and head to the beach.

See 2018 program

Travel to Hydra

Hydra is a small island in the Argo Saronic Gulf, lying off the east coast of the Peloponnese and easily reached by hydrofoil from the Athens port of Piraeus.

Travel information

Accommodations

The meeting is held at the Bratsera Hotel. A wide range of accommodation is available within 5-10 minutes walk of the conference venue, including pensions for those on a tight budget.

Accommodations

Organizing Committee

Dick Davis, University of Colorado
Kleoniki Gounaris, Imperial College
Rick Maizels, University of Glasgow
Murray Selkirk, Imperial College

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