We are pleased to announce the 11th release of WormBase ParaSite. We have added data, new functionality, and improved some of our per-release processes. Quite a few genomes are new or have been significantly updated.
Comments in ParaSite
By popular request we have added a comment-like space to our gene pages. You can mention your own results, point out an inconsistency, or make an observation about displayed data. We hope the comments will be of scientific content, even when taking a lighter form than communication through peer-reviewed journals.
New species and updates
We are updating three flatworm genomes:
The new assembly of S. mansoni is very complete and accurate, and the gene models were manually annotated over the course of several months.
This is the list of our new or updated nematode genomes:
We are also publishing a fix from the authors to their annotation of Ascaris suum and Parascaris univalens. The gene models submitted to us in the previous release suffered from a systematic error, which resulted in much shorter proteins. We regret the error.
Additionally, the release includes genomes from the WS265 release of WormBase, including the newest WormBase core species, Trichuris muris.
In total 17 genomes were added or changed, bringing the total to 148 genomes across 124 species.
We ran all our usual tertiary annotation pipelines that identify repeats, low complexity regions, non-coding RNAs, protein domains, predicted GO terms, and more, as well as our comparative genomics pipeline, where we expect an improvement especially around recently updated branches.
We have revisited our cross-references pipeline. This pipeline lets us support discovery of what is currently known about each gene, and provide rich descriptions, through inferring links between our genes and entities from other resources. We have updated these cross-references for all our genomes, and added new references: to UniParc and RNAcentral. You can either find these references on the gene pages, or use BioMart to retrieve them in bulk.
We have configured our JBrowse track displays to include tracks with aligned reads produced by the RNASeq-er project. RNASeq-er processes all RNASeq datasets published in ENA, so there are many tracks to choose from: currently 11735, from 492 studies across 74 species.
Use case 1 : discover public datasets
Browsing our displays could be an alternative to searching a primary source like the European Nucleotide Archive, benefiting from an additional filter: they include only the runs that RNASeq-er successfully aligned and passed through QC.
For more than half the species, the only RNASeq data available is what was produced while preparing the genome.
For other species, there have been additional studies, for example see the JBrowse display of tapeworm Echinococcus multilocularis. Apart from a few studies from the same lab in the United Kingdom where the genome was sequenced, the display contains runs sequenced in China and Japan as part of BioProjects PRJNA254535 and PRJDB3524.
The WormBase ParaSite species with most RNASeq data present is unsurprisingly C. elegans, with 6446 runs across 245 studies.
Use case 2 : compare expression across tracks
Consider the gene Smp_169190 in Schistosoma mansoni. Lu et al (2018, preprint) compared expression in developmental stages, and found Smp_169190 to be differentially expressed in the cercarial life stage.
This link here takes you to two of the tracks used in Lu et al’s metaanalysis. These are ERR022872, showing RNA sequenced from cercaria, and a track ERR506086, with RNA sequenced from an an adult worm. The two tracks differ in expression dramatically in gene Smp_169190.
You can also see the expression in other life stages. A search for “cercaria” shows quite a few tracks, that will probably be similar to ERR022872. Similar search for “miracidia” yields a track SRR922067 and an interesting result: miracidia don’t express Smp_169190, but there is high expression for two of the nearby TAL genes.