Author: Faye Rodgers

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.

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:

• 5 Panagrolaimus/Propanagrolaimus species, including the Antarctic nematode Panagrolaimus davidi, from Schiffer et al., 2019.
• 10 new Caenorhabditis species from Stevens et al., 2019 and Stevens et al, 2020.
• Setaria digitata, a filarial parasite of ungulates, from Rashanthy Nadarajah and colleagues of the University of Colombo.
• The large liver fluke Fasciola gigantica, from The Genome Institute.
• The lung fluke Paragonimus westermani, from Oey et al., 2019.
• The cestode Echinococcus oligarthrus, from Moldanado et al., 2019

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.

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!

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 [email protected] 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).

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/