Difference between revisions of "WormBase Genomes"

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Revision as of 09:57, 24 September 2010

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
II Yes Yes WashU
II Yes Yes WashU
II Yes Yes WashU
II Yes Yes WashU
II Yes Yes WashU
II Yes Yes WashU
II Yes Yes WashU
II Yes Yes WashU
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)