WormBase release WS247

Orthology update

* Data from Inparanoid was updated to version 8
* Orthology data for all core nemtatodes and model organisms was imported from WormBase Parasite release 1
* OMA and TreeFam data was removed in preparation for an update (TreeFam accessions will remain as database crossreferences)

Expression and Picture update

* A large set of expression graphs for other nematodes produced by Yanai’s has been added

RNASeq data

The RNASeq data will become richer in WS247.

There will also be “control” mean and median FPKM values derived from the data which does not have a specific experimental condition applied.

New/updated reference genomes

This release we see a rebuild of C. elegans, B. malayi and O. volvulus. Various data classes and curational activites have been undertaken on these species since the release of WS246

Announcing WormBase ParaSite

Parasitic worms (helminths) are responsible for more than a billion human infections globally and have a devastating impact on livestock and agriculture. As international efforts to sequence the genomes of parasitic helminths gather pace, the WormBase groups at EMBL-EBI and Wellcome Trust Sanger Institute have collaborated on the creation of a new BBSRC-funded resource, WormBase ParaSite, to analyse, store and present information on these genomes. WormBase ParaSite is closely integrated with and complementary to the main WormBase web-site, the central mission of which is to support researchers using Caenorhabditis elegans as a model system.

The first release of WormBase ParaSite includes annotated genomes from 82 species (57 nematodes and 25 platyhelminths), with features including:

  • A genome browser for every genome
  • Comparative analysis (gene orthology and paralogy) using the Ensembl Compara Gene Tree inference method
  • Full text and sequence search (BLAST) services

Development in the coming months will see improved cross-linking to and from the main WormBase site, incorporation of new genomes and data sets, and new querying interfaces and tools oriented towards the use-cases of parasitologists.

Trichuris suis

A new genome of a zoonotic whip worm species, Trichuris suis, has been made publicly available by the Gasser lab of Melbourne University.

As part of the research into the unique properties of the genome, a male and a female worm has been sequenced, assembled and annotated as described in Genome and transcriptome of the porcine whipworm Trichuris suis. Jex AR, Nejsum P, Schwarz EM, Hu L, Young ND, Hall RS, Korhonen PK, Liao S, Thamsborg S, Xia J, Xu P, Wang S, Scheerlinck JP, Hofmann A, Sternberg PW, Wang J, Gasser RB. Nat Genet. 2014 Jul;46(7):701-6. doi: 10.1038/ng.3012. Epub 2014 Jun 15.

It has been included as part of the WS243 release of WormBase and is shown on a Genome Browser, as well as on orthology sections of genes. Flatfiles of the raw data are also available on ftp://ftp.wormbase.org.

Ancylostoma ceylanicum

The parasitic nematode Ancylostoma ceylanicum is a hookworm, closely related to the hookworms Ancylostoma duodenale and to Necator americanus.

These three species collectively infect over 500 million human beings, typically by burrowing into the skin as dauer-like L3 larvae, passing through the bloodstream and lungs, being swallowed along with mucus cleaning the lungs, and becoming permanently established as blood-drinking adults in the small intestine.

Despite the great difference in their life cycles from that of C. elegans, hookworms (and related parasites such as Haemonchus contortus) are actually more closely related to C. elegans than is the free-living nematode Pristionchus pacificus.

The bulk of hookworm infections are by A. duodenale and N. americanus; however, these two species do not generally infect other mammals, making them difficult to study experimentally. In contrast, A. ceylanicum competently infects humans, dogs, cats, and golden hamsters, making it an experimentally tractable human hookworm as well as an emerging zoonotic parasite (http://www.ncbi.nlm.nih.gov/pubmed/23968813). Researchers at Cornell, Caltech, and UCSD have therefore sequenced the genome and transcriptome of A. ceylanicum in order to determine possible new targets for drugs and vaccines.

Its genome has been included as part of the WS243 release of WormBase and is shown on a Genome Browser, as well as on orthology sections of genes. Flatfiles of the raw data are also available on ftp://ftp.wormbase.org.

new Pristionchus species in WS243

Thanks to the contribution of new sequencing data on Pristionchus spp. populations as described in “Characterization of genetic diversity in the nematode Pristionchus pacificus from population-scale resequencing data” by Christian Roedelsperger, et.al, published in Genetics, the next WormBase release (WS243) will include Pristionchus exspectatus as a new species.

The new data will be available through the FTP site, a Genome Browser and as orthologs from already existing gene pages.