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| | == WormBase Genomes == | | == WormBase Genomes == |
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| − | This is a record of the current and proposed set of genomes in WormBase.
| + | An up to date list of genomes in WormBase can be found at: http://www.wormbase.org/species/all |
| | | | |
| − | === Tiers === | + | == See also == |
| | | | |
| − | '''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. | + | *[[Caenorhabditis elegans|''Caenorhabditis elegans'']] |
| | + | **[http://en.wikipedia.org/wiki/Caenorhabditis_elegans Wikipedia entry on ''C. elegans''] |
| | + | ** [[About elegans|''About C. elegans'']] |
| | + | **[[Key publications|Key publications]] |
| | + | **[[Nomenclature|Genetic Nomenclature]] |
| | + | **[[Other nematodes|Other nematodes]] |
| | + | **[[Nematode sequencing summary|Nematode resequencing and diversity]] |
| | + | **[[Partslist|The C. elegans Parts List (List of Cells)]] |
| | + | *[[Possible_assembly_errors]] - in all Caenorhabditis species |
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| − | '''Tier II''' - Efforts are made, where practical, to manually curate the gene structure and possibly some other genomic information.
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| | | | |
| − | '''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.
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| | | | |
| − | '''Tier IV''' - Proposed tier for organisms with only transcriptome information and no coherent genome. There are no examples of this at present.
| + | [[Category:User Guide]] |
| − | | |
| − | === Genome ===
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| − | | |
| − | The '''Genome''' column in the table indicates whether the genome has been added to WormBase.
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| − | | |
| − | === Gene ===
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| − | | |
| − | The '''Genes''' column in the table indicates whether gene structures have been predicted.
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| − | | |
| − | === The genome status ===
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| − | | |
| − | {| class="wikitable" border="1"
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| − | |-
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| − | ! Species
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| − | ! NCBI TaxonID
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| − | ! Tier
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| − | ! Genome
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| − | ! Genes
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| − | ! Origin
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| − | ! Comments
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| − | |-
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| − | | Caenorhabditis briggsae
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| − | | 6228
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| − | | II
| |
| − | | Yes
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| − | | Yes
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| − | | WashU
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| − | | New assembly from Erich Haag Sept 2010
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| − | |-
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| − | | Caenorhabditis remanei
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| − | | 31234
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| − | | II
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| − | | Yes
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| − | | Yes
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| − | | WashU
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| − | |
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| − | |-
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| − | | Caenorhabditis brenneri<br>(Species 4)
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| − | | 135651
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| − | | II
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| − | | Yes
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| − | | Yes
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| − | | WashU
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| − | | A lot of heterozygosity.
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| − | |-
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| − | | '''Caenorhabditis elegans strain N2'''
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| − | | 6239
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| − | | I
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| − | | Yes
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| − | | Yes
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| − | | WashU/Hinxton
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| − | |
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| − | |-
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| − | | Caenorhabditis elegans strain DR1035
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| − | | 6239
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| − | | III
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| − | |
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| − | |
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| − | | Mark Blaxter
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| − | | status unclear
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| − | |-
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| − | | Caenorhabditis japonica
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| − | | 281617
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| − | | II
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| − | | Yes
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| − | | Yes
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| − | | WashU
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| − | |
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| − | |-
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| − | | Caenorhabditis species 3 strain PS1010
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| − | | 9668
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| − | | II
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| − | | Yes
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| − | | Yes
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| − | | CalTech
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| − | |
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| − | |-
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| − | | Heterorhabditis bacteriophora'
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| − | | 37862
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| − | | III
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| − | |
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| − | |
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| − | | WashU
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| − | |-
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| − | |
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| − | |
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| − | | II
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| − | | Yes
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| − | | Yes
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| − | | WashU
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| − | |-
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| − | |
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| − | |
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| − | | II
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| − | | Yes
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| − | | Yes
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| − | | WashU
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| − | |-
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| − | |
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| − | |
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| − | | II
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| − | | Yes
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| − | | Yes
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| − | | WashU
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| − | |-
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| − | |
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| − | |
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| − | | II
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| − | | Yes
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| − | | Yes
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| − | | WashU
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| − | |-
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| − | |
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| − | |
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| − | | II
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| − | | Yes
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| − | | Yes
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| − | | WashU
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| − | |-
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| − | |
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| − | |
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| − | | II
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| − | | Yes
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| − | | Yes
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| − | | WashU
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| − | |-
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| − | |
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| − | |
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| − | | II
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| − | | Yes
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| − | | Yes
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| − | | WashU
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| − | |-
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| − | |
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| − | |
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| − | | II
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| − | | Yes
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| − | | Yes
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| − | | WashU
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| − | |-
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| − | |
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| − | |
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| − | | II
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| − | | Yes
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| − | | Yes
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| − | | WashU
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| − | |
| |
| − | |}
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| − | | |
| − | === Phylogeny ===
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| − | | |
| − | Given my understanding of the current phylogenetic literature, the correct guide tree would be:
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| − | | |
| − | ((((((((C._briggsae,C._remanei),C._brenneri),C._elegans),C._japonica),H._contortus),P._pacificus),(M._hapla,M._incognita)),,B._malayi)
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