For miRNA fans

For miRNA fanatics out there, we have added 90 miRNA gene clusters from MirGeneDB to the C. elegans annotation in release WS284. This complements the 20 clusters (800 objects) which were already there, making the WormBase miRNA collection possibly the most complete in the world. You can access the miRNAs through the web pages https://wormbase.org/search/all/miRNA, or through JBrowse tracks “Curated Genes(noncoding)” e. g. And don’t forget WormBase also has an impressive collection of other non-coding RNAs as well; circRNAs, lincRNAs, piRNAs, snRNA, snoRNAs, precursors and many more. Happy investigating!

New operons in C. briggsae

Kindly, Dr. Itai Antoine Toker made us aware of the paper Uyar et al. Genome Research 2012 (PMID: 22772596/ WBPaper00041271), which contains a genome-wide set of operon predictions for C. briggsae. The data was mapped forward to the current gene set using the Sequence IDs supplied. 1034 operons were captured from the publication, but because of the time between publication and extensive re-annotation of C. briggsae only 709 of these operons had enough information to allow us to map them precisely onto the genome and supplement the C. briggsae operon JBrowse track. If you find some interesting dataset you’d like WormBase to curate, please let us know at help@wormbase.org

3D structures for all proteins

AlphaFold is an AI system, created in partnership between DeepMind and the EMBL-European Bioinformatics Institute (EMBL-EBI), that makes predictions of a protein’s structure from its amino-acid sequence. Go to their webpage to look at your favourite protein from C. elegans, Brugia, Onchocerca, Strongyloides, Trichuris or Wuchereria. If your favourite protein is missing, remember that any protein with >90% amino acid similarity is quite likely to have a very similar structure. And if you spot any structure that does not look right contact help@wormbase.org, and we’ll forward your feedback.

Two new genes in C. elegans!

After more than 20 years of careful manual curation of C. elegans, it is quite unusual to find new protein-coding genes. But in release WS283 we have no less than 2 new genes! We were alerted to the first one by Dr. Adam Norris from Southern Methodist University, Dallas, TX, USA. Working with WormBase curators, we were able to comprehensively annotate the new gene. As finding a new gene is such a remarkable event, Dr. Norris opted for writing a micropublication describing the new gene WBGene00306123 (Y97E10C.2). Iyengar, A; Diamantakis, S; Norris, A (2021), “A new gene on C. elegans chromosome V

Buoyed by the first discovery, WormBase curators looked through our curation records and found a second new gene to annotate: WBGene00306124 (W04B5.9). Both of these new genes are in release WS283, and we look forward to learning even more about the biology of these new genes.

If you happen to spot what you think is a new gene – please email help@wormbase.org to let our curators know about it!

WormBase release WS282

New release of Wormbase WS282 is out. Details related to the data and changes in WS282 are available in the release notes.

A highlight of this release is that variant data are now also available in VCF file format:

c_elegans.PRJNA13758.WS282.variations.vcf.gz and c_briggsae.PRJNA10731.WS282.variations.vcf.gz

These files are available in the respective “species” folder on the WormBase FTP site.