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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 ===
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| − | | |
| − | '''Tier I''' - All efforts are made to curate the gene structures and any other genetic or metabolic information. Only '''C. elegans''' is in this group.
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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.
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| − | | |
| − | === 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 added to WormBase.
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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
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| − | | Yes
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| − | | Yes
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| − | | WashU
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| − | | [Sept 2010] New assembly from Erich Haag being worked on.
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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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| − | |-bgcolor="#00D7D7"
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| − | | [[Caenorhabditis elegans|''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/Sanger
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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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| − | | Pristionchus pacificus
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| − | | 54126
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| − | | II
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| − | | Yes
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| − | | Yes
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| − | | WashU
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| − | | [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."
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| − | |-
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| − | | Haemonchus contortus
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| − | | 6289
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| − | | III
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| − | | Yes
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| − | | Yes
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| − | | Sanger
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| − | | Added to WormBase in release WS209.
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| − | |-
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| − | | Strongyloides ratti
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| − | | 34506
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| − | | III
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| − | |
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| − | |
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| − | | Sanger
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| − | | [30 June 2010] Assembly due out in mid 2011. They 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.
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| − | |-
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| − | | Meloidogyne hapla
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| − | | 6305
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| − | | III
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| − | | Yes
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| − | | Yes
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| − | | NCSU hapla.org
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| − | | Added to WormBase in release WS204.
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| − | |-
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| − | | Meloidogyne incognita
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| − | | 6306
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| − | | III
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| − | | Yes
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| − | |
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| − | | INRA
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| − | | Added to WormBase in release WS205. Genes are not yet available.
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| − | |-
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| − | | [[Brugia malayi|''Brugia malayi'']]
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| − | | 6279
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| − | | III
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| − | | Yes
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| − | | Yes
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| − | | TIGR -> WashU/Sanger
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| − | | [Sept 2010] Currently using the old TIGR assembly. Waiting for WashU (did assembly) and Sanger (did gene models) to publish, then we will use the new assembly
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| − | |-
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| − | | Onchocerca volvulus
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| − | | 6282
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| − | | III
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| − | |
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| − | |
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| − | | Sanger
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| − | |
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| − | |-
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| − | | Ascaris suum
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| − | | 6253
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| − | | III
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| − | |
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| − | |
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| − | | Sanger
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| − | |
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| − | |-
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| − | | Globodera pallida
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| − | | 36090
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| − | | III
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| − | |
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| − | |
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| − | | Sanger
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| − | |
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| − | |-
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| − | | Nippostrongylus brasiliensis
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| − | | 27835
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| − | | III
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| − | |
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| − | |
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| − | | Sanger
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| − | |
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| − | |-
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| − | | Strongyloides ransomi
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| − | | 553534
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| − | | III
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| − | |
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| − | |
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| − | | Sanger
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| − | | (Not sure if the name is right, I copied it down in the lecture as 'S. mansoni')
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| − | |-
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| − | | Teladorsagia circumcincta
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| − | | 45464
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| − | | III
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| − | |
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| − | |
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| − | | Sanger
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| − | |
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| − | |-
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| − | | Trichuris muris
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| − | |
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| − | | III
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| − | |
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| − | |
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| − | | Sanger
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| − | |
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| − | |-
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| − | | Trichinella spiralis
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| − | | 6334
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| − | | III
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| − | |
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| − | |
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| − | | WashU
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| − | | [Sept 2010] Being assembled.
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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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| − | | |
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| | == See also == | | == See also == |
