|
|
(181 intermediate revisions by 3 users not shown) |
Line 1: |
Line 1: |
| == WormBase Genomes == | | == WormBase Genomes == |
| | | |
− | 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 |
| | | |
− | '''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.
| + | [[Category:User Guide]] |
− | | |
− | === 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 ===
| |
− | | |
− | {| class="wikitable" border="1"
| |
− | |-
| |
− | ! 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<br>(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
| |
− | |
| |
− | |-
| |
− | |
| |
− | |
| |
− | | 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
| |
− | |-
| |
− | |
| |
− | |
| |
− | | 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)
| |