WormBase Genomes

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WormBase Genomes

This is a record of the current and proposed set of genomes in WormBase.

Tiers

Tier I - All efforts are made to curate the gene structuers and any other genetic or metabolic information. Only C. elegans is in this group.

Tier II - Efforts are made, where practical, to manually curate the gene structure and possibly some other genomic information.

Tier III - We will set up the genome on WormBase with any gene structures that the authors of this genome have predicted. No further curation efforts are made by the WormBase consortium.

Tier IV - Proposed tier for organisms with only transcriptome information and no coherent genome. There are no examples of this at present.

Genome

The Genome column in the table indicates whether the genome has been added to WormBase.

Gene

The Genes column in the table indicates whether gene structures have been predicted.

The genome status

Species NCBI TaxonID Tier Genome Genes Origin Comments
Caenorhabditis briggsae 6228 II Yes Yes WashU New assembly from Erich Haag Sept 2010
Caenorhabditis remanei 31234 II Yes Yes WashU
Caenorhabditis brenneri
(Species 4)
135651 II Yes Yes WashU A lot of heterozygosity.
Caenorhabditis elegans strain N2 6239 I Yes Yes WashU/Hinxton
Caenorhabditis elegans strain DR1035 6239 III Mark Blaxter status unclear
Caenorhabditis japonica 281617 II Yes Yes WashU
Caenorhabditis species 3 strain PS1010 9668 II Yes Yes CalTech
Heterorhabditis bacteriophora 37862 III WashU
Pristionchus pacificus 54126 II Yes Yes WashU [21 June 2010] Christophe Dietrich says "he will switch to the new assembly which is not in Genbank but part of PubMed 20237107. Move the old gene predictions and corrections to new assembly. There is 454 data as well. New assemblies will be made as he has time."
Haemonchus contortus 6289 III Yes Yes Sanger Added to WormBase in release WS209.
Strongyloides ratti 34506 III Sanger Assembly due out in mid 2011. Have fosmid & BAC libraries. Have ~5000 contigs and ~99% of genome done. Have about 10,000 genes which is the expected number as it is half the size of C. elegans.
Meloidogyne hapla 6305 III Yes Yes NCSU hapla.org Added to WormBase in release WS204.
Meloidogyne incognita 6306 III Yes INRA Added to WormBase in release WS205. Genes are not yet available.
Brugia malayi 6279 III Yes Yes TIGR -> WashU/Sanger Currently using the old TIGR assembly. Waiting for WashU (did assembly) and Sanger (did gene models) to publish.
Onchocerca volvulus 6282 III Sanger
Ascaris suum 6253 III Sanger
II Yes Yes WashU
II Yes Yes WashU

Phylogeny

Given my understanding of the current phylogenetic literature, the correct guide tree would be:

   ((((((((C._briggsae,C._remanei),C._brenneri),C._elegans),C._japonica),H._contortus),P._pacificus),(M._hapla,M._incognita)),,B._malayi)