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)