Guest Blog: New Nematodes in WormBase

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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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Check out the Eukaryotic Genomic Databases book!

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The Eukaryotic Genomic Databases book has just been released by Springer (Editors: Kollmar, Martin) and contains detailed chapters related to the eukaryotic databases such as WormBase, FlyBase, the yeast databases, SGD and PomBase, etc. The chapters describe database contents and classic use-cases, which assist in accessing eukaryotic genomic data and encouraging comparative genomic research.

WS264 release

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C. elegans sORFs

sORFs.org 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.

Include strain names in publications!

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We urge you to explicitly state strains used in your experiments to foster reproducibility and to help WormBase biocurators get your results into WormBase.

 Historically, C. elegans researchers just stated the alleles used, based on the reasonable idea that all strains were close to Brenner’s N2.  As the years and hundreds of worm generations passed, strains diverged.  We usually don’t know the full genotype of our strains (and really won’t even with whole genome sequencing since copy number variation is often hard to detect). Including strain names will greatly help sort out any background effects that are realized later.

 We thus would like to see editors and reviewers (both anonymous and within the laboratory) help enforce the inclusion of strain names in C. elegans papers.

-Paul Sternberg

Wondering how to cite WormBase?

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If you are looking to cite WormBase please take a look at: https://wormbase.org/about/citing_wormbase#012–10. This can also be accessed from the Menu at the bottom of the WormBase home page on the extreme left, under WormBase–>How to cite.  Please do explicitly acknowledge WormBase in your published work when you have used it in the planning, design, execution, analysis, or reporting of the research described.  We can then search for these acknowledgements and use these numbers in various reports, eg. for funding agencies, etc.