Guest Blog: New Nematodes in WormBase


This WS264 release of WormBase includes two new genome assemblies from both a free-living Caenorhabditis species (C. nigoni) and a whipworm parasite of mice (Trichuris muris).

The C. nigoni genome was assembled from both long-read (Pacific Biosciences) and short-read (Illumina) data, and then further scaffolded by genome-wide alignment with its very close relative, C. briggsae.

Despite the fact that C. nigoni and C. briggsae are closely enough related to produce partially fertile offspring, their lifestyles and genomes are quite different.  C. briggsae, like C. elegans, is primarily a self-fertilizing hermaphrodite with roughly 1% males.  C. nigoni, in contrast, is like most animal species (including humans) and has 50% males with 50% females.  At the molecular level, C. nigoni‘s genome is larger than that of C. briggsae (130 Mb versus 108 Mb) and encodes 7,000 more genes, which appear to have been lost in C. briggsae after it evolved hermaphroditism, and which disproportionately encode small proteins with male-biased expression.

The T. muris genome was assembled from long-read (Pacific Biosciences) and short-read (Illumina) data, with the help of an optical map.

T. muris infects the caecum region of the mouse large intestine, and is very closely related to the human whipworm parasite T. trichiura, for which T. muris is a laboratory model.  Adult whipworms have a highly unusual body shape for nematodes: their heads and front bodies have a whip-like shape that can be inserted into intestinal cells like a flexible needle, and that is easily mistaken as a “tail” rather than the worm’s head.  Whipworm heads have a specific ultrastructure called a “stichosome” that allows them both to suck nutrients out of intestinal cells and to export immunosuppressive molecules into their hosts.  This strategy is unfortunately effective: over 700 million human beings are currently infected by T. trichiura.  Having a high-quality genome assembly for T. muris raises the hope of rational interventions against this worldwide parasite.

guest authors: Faye Rogers(1) and Erich Schwarz(2)

(1) Wellcome Sanger Institute

(2) Cornell University


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WS264 release

C. elegans sORFs is a public repository of small open reading frames (sORFs) identified by ribosome profiling (RIBO-seq).

It contains predicted sORF regions for several species, including C. elegans.

We have annotated 118 predicted sORF regions as coding (CDS) isoforms of the existing genes. It is likely that in the next release, where these isoforms do not overlap with existing isoforms, these sORF regions will be changed to be individual genes and not isoforms.

52 of these annotated sORF regions do not start with the canonical Methionine AUG initiation codon. It is possible that they use a non-canonical initiation codon. Some of these non-canonical initiation codons are not the expected non-canonical initiation codon Isoleucine, but code for residues like Valine.

Trichuris muris

This release we see the integrated of the Edinburgh strain of Trichuris muris version TMUE3.1. This species has been fully integrated as a core species meaning there are stable IDs and tracking with inclusion in all additional pipelines and analysis.
The genome assembly and gene annotation has been taken directly from the Pathogen Genomics group at the WTSI. Additional mapping of gene mergers, splits and transfer of IDs from the TMUE2.2 has been done to allow users to identify their genes of interest.

Caenorhabditis nigoni

This release includes the Caenorhabditis nigoni genome assembly and gene set described in “Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins” by Da Yin, et. al (Science 359,55-61 2018) as non-core species set.
This species should be of special interest, due to its phylogenetic closeness to C.briggsae and its differences in sexual reproduction.

The data is available as files on the WormBase FTP site, as well as the JBrowse genome browser.

WormBase Release WS263

We would like to announce the availability of the WormBase WS263 release on the WormBase website and FTP.

Some of the highlights of this release are:

New Pristionchus Assembly and Gene Set

The new data made available through WormBase is described in “Single-Molecule Sequencing Reveals the Chromosome-Scale Genomic Architecture of the Nematode Model Organism Pristionchus pacificus by Christian Roedelsperger, et al. in Cell.

ID mapping was carried out to try and preserve the existing IDs. The published IDs were also incorporated into the database so that they are searchable on

New PantherDB data

the PantherDB orthology set included in WormBase has been updated to the latest version (13.0).

DNAseI hypersensitive Sites

We have created 42,728 Features with a Method=DNAseI_hypersensitive_site to mark DNase hypersensitivity sites found in C. elegans ’embryo’ and ‘L1 arrest’ life-stages in non-coding regions from the paper WBPaper00053259. These sites, together with Transcription Factor footprints, will be added to the tracks available in the genome browsers.

Genome Res. 2017 Dec;27(12):2108-2119. “Genome-wide discovery of active regulatory elements and transcription factor footprints in Caenorhabditis elegans using DNase-seq.”  Ho MCW, Quintero-Cadena P, Sternberg PW.

ParaSite Release 3

We are pleased to announce the third release of WormBase ParaSite, the home for parasitic worm draft genomes and genomic data in WormBase.

This release includes two new annotated genomes, taking the total number of nematode and flatworm genomes in WormBase ParaSite to 99, representing 90 species. The new genomes are:

  • Echinococcus canadensis (PRJEB8992)
  • Loa loa (PRJNA246086)

This release also includes a REST API, providing language-neutral programmatic access to ParaSite data via a RESTful interface (, and an improved BLAST search which is faster and has no limit on the number of species that can be BLASTed against (

Finally, in this release we are displaying tapeworm RNASeq data for the species Echinococcus granulosus, Echinococcus multilocularis and Hymenolepis microstoma (as example). We will be including more transcriptomic data sets in upcoming ParaSite releases so if you would like to suggest datasets you would like to see displayed please get in touch!