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 wormbase.org.

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 (http://parasite.wormbase.org/api/), and an improved BLAST search which is faster and has no limit on the number of species that can be BLASTed against (http://parasite.wormbase.org/Tools/Blast).

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!

WS249: reorganization of parasitic non-core species

Starting with the WS249 release of WormBase we will point users to the new WormBase ParaSite portal for parasitic nematodes that are not curated as part of the WormBase core species.

Species that can now be found at WormBase ParaSite are:
Ancylostoma ceylanicum (PRJNA231479|PRJNA72583)
Ascaris suum (PRJNA62057|PRJNA80881)
Bursaphelenchus xylophilus (PRJEA64437)
Dirofilaria immitis (PRJEB1797)
Haemonchus contortus (PRJEB506|PRJNA205202)
Loa loa (PRJNA60051 )
Meloidogyne hapla (PRJNA29083)
Meloidogyne incognita (PRJEA28837)
Necator americanus (PRJNA72135)
Trichinella spiralis (PRJNA12603)
Trichuris suis (PRJNA179528|PRJNA208415|PRJNA208416)

WS249: Parasite Papers II

For the upcoming WS249 release, a set of new papers have been added to the WormBase database. Some papers of interest to the parasite community are shown below.

Rateb ME, Yang D, Vodanovic-Jankovic S, Yu Z, Kron MA, Shen B.Adipostatins A-D from Streptomyces sp. 4875 inhibiting Brugia malayi asparaginyl-tRNA synthetase and killing adult Brugia malayi parasites. J Antibiot (Tokyo). 2015

Referenced Genes: Bma-nars-2

Yang Y, Wen Yj, Cai YN, Vallée I, Boireau P, Liu MY, Cheng SP.Serine proteases of parasitic helminths. Korean J Parasitol. 2015 Feb;53(1):1-11.

Referenced Genes: Bm10893, Bm4862, OVOC9258, OVOC9605

O’Connell EM, Bennuru S, Steel C, Dolan MA, Nutman TB.Targeting Filarial Abl-like Kinases: Orally Available, Food and Drug Administration-Approved Tyrosine Kinase Inhibitors Are Microfilaricidal and Macrofilaricidal. J Infect Dis. 2015 Feb 5.

Referenced Genes: OVOC2839, Bm3303, Bm3304