Difference between revisions of "LIST OF AVAILABLE CAENORHABDITIS SPECIES and the state of their genome projects"
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− | ! Species !! Reference strain !! Reproduction !! Collector !! Location !! Date !! Isolated by !! Phylogenetic affiliation !! Geographic distribution and available isolates (lab) !! Inbred strain !! Genome project | + | ! Species !! Reference strain !! Reproduction !! Collector !! Location !! Date !! Isolated by !! Phylogenetic affiliation !! Geographic distribution and available isolates (lab) !! Inbred strain !! Genome project see the Blaxter lab project page http://nematodes.org/genomes/index_caenorhabditis.html) |
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| '''''angaria''''' || PS1010 || F/M || || ||1990 || || ''Drosophilae'' super-group, ''Angaria'' group || 3 isolates from Florida USA || - || formerly ''C.'' sp. 3; Mortazavi et al. 2010 Genome Research, '''@Wormbase''' | | '''''angaria''''' || PS1010 || F/M || || ||1990 || || ''Drosophilae'' super-group, ''Angaria'' group || 3 isolates from Florida USA || - || formerly ''C.'' sp. 3; Mortazavi et al. 2010 Genome Research, '''@Wormbase''' |
Revision as of 16:40, 29 August 2014
Species | Reference strain | Reproduction | Collector | Location | Date | Isolated by | Phylogenetic affiliation | Geographic distribution and available isolates (lab) | Inbred strain | Genome project see the Blaxter lab project page http://nematodes.org/genomes/index_caenorhabditis.html) | |
---|---|---|---|---|---|---|---|---|---|---|---|
angaria | PS1010 | F/M | 1990 | Drosophilae super-group, Angaria group | 3 isolates from Florida USA | - | formerly C. sp. 3; Mortazavi et al. 2010 Genome Research, @Wormbase | ||||
brenneri | F/M | Elegans group | tropical, ~30 isolates (Felix, Cutter, Braendle) | PB2801 | Wash U, @Wormbase | ||||||
briggsae | AF16 | H/M | Elegans group | world-wide distribution, 100s of isolates | N.A. | Stein et al. 2003 PLoS Biology, @Wormbase | |||||
drosophilae | DF5077 | F/M | Drosophilae group | rotting saguaro cactus in Arizona, a few isolates | DF5112 | ||||||
elegans | N2 | H/M | Elegans group | world-wide (mostly temperate) distribution, 100s of isolates | N.A. | C. elegans Sequencing Consortium 1998 Science, @Wormbase | |||||
japonica | F/M | Elegans super-group, Japonica group | isolates from Japan (Yoshiga/Cutter) | DF5080 | Wash U, @Wormbase | ||||||
plicata | SB355 | F/M | Blaxter, in process | ||||||||
remanei | F/M | Elegans group | USA/Canada, Europe, Japan, Taiwan, 100s of isolates | PB4641 | Wash U, @Wormbase | ||||||
sp. 1 | SB341 | F/M | S. Wirth | Berlin, Germany | 2000? | W. Sudhaus | base of Caenorhabditis | 1 single isolate | JU1667 | Félix/Blaxter preliminary assembly http://nematodes.org/genomes/caenorhabditis_sp1/ | |
sp. 2 | DF5070 | F/M | S. Wirth | Corsica, France | Oct 2001 | W. Sudhaus | Drosophilae group, sister of C. drosophilae | 1 single isolate | |||
sp. 5 | JU727 | F/M | M.-A. Félix | Chengyang, Guangxi, China | 6 May 2005 | M.-A. Félix | Briggsae subgroup | Isolates from China, Vietnam (Cutter, Ailion, Félix) | JU800 | Cutter/Blaxter, @Wormbase | |
portoensis (ex-sp. 6) | EG4788 | F/M | M. Ailion, A.-J. Rodrigues | Amares, Portugal | 28 Mar 2007 | M. Ailion | Drosophilae super group | Portugal, Spain, France, Ireland (Ailion, Félix, Braendle) | EG5626 | ||
afra (ex-sp. 7) | JU1199 | F/M | M. Herrmann | Begoro, Ghana | Jun 2007 | M.-A. Félix | Japonica group | 2 isolates from West Africa (Félix) | JU1286 | Wash U CONTAMINATED WITH SP. 9 www.nematodes.org/nematodegenomes/index.php/959_Nematode_Genomes | |
sp. 8 | QX1182 | F/M | M. Rockman | Backyard of 93 Mercer St., Jersey City, NJ, USA | 28 Jul 2007 | M. Rockman | Angaria group | Isolates from USA (Fitch), Europe (Braendle, Félix), Canada (Rockman) | |||
nigoni (ex-sp. 9) | JU1325 | F/M | M.-A. Félix | Trivandrum Zoo, Kerala, India | 21 Dec 2007 | M.-A. Félix | Briggsae subgroup | Various wet tropical places from Yucatan to Singapore (Ailion, Félix, Inoue) | JU1422 | (Wash U: contaminated genomic, cDNAs OK) Resequenced by Barbara Meyer | |
doughertyi (ex-sp. 10) | JU1323 | F/M | M.-A. Félix | Angela Spice Garden, Kerala, India | 27 Dec 2007 | M.-A. Félix | Brenneri subgroup | 6 isolates from South India | JU1771 | Blaxter, in process | |
tropicalis (ex-sp. 11) | JU1373 | H/M | V. Robert, L. Sablé | Saint-Benoît, La Réunion | Jan 2008 | M.-A. Félix | Brenneri subgroup | Common in tropical regions (not so far on the African continent, one in Asia) | N.A. | Wash U, @Wormbase | |
castelli (ex-sp. 12) | JU1426 | F/M | P. Châtelet | Nouragues Forest, French Guiana | May 2008 | M.-A. Félix | Angaria group | 2 isolates from French Guiana | JU1956 | Blaxter, in process | |
virilis (ex-sp. 13) | JU1528 | F/M | M.-A. Félix | Orsay apple orchard | 9 Sep 2008 | M.-A. Félix | Drosophilae super group | A few isolates, all from Orsay, France | JU1968 | Richaud/Félix prepping DNA/RNA for Blaxter | |
imperialis (ex-sp. 14) | EG5716 | F/M | D. Ailion | Moorea, French Polynesia | 24 Jul 2009 | M. Ailion | Japonica group | also Polynesia, Guadeloupe (Félix, Braendle) | EG5942-EG5947 | ||
kamaaina (ex-sp. 15) | QG122 | F/M | M. Rockman | Near Hanalei Bay, Kauai, Hawaii, USA | 2 Aug 2009 | M. Rockman | Elegans super group | Kauai and Maui, 2 isolates | QG2076, QG2077 | under assembly, Rockman | |
wallacei (ex-sp. 16) | JU1873 | F/M | J.-B. Pénigault | Sanda Center, Bali, Indonesia | 11 Nov 2009 | J.-B. Pénigault | Brenneri subgroup | 2 isolates from Indonesia (Félix) | JU1898 | Félix/Blaxter preliminary assembly available-ask us | |
nouraguensis (ex-sp. 17) | JU1825 | F/M | C. Braendle, M.-A. Félix | Nouragues Forest, French Guiana | 21 Nov 2009 | C. Braendle, M.-A. Félix | Japonica group | Many isolates from French Guiana | JU2079 | planning Ailion | |
macrosperma (ex-sp. 18) | JU1857 | F/M | C. Braendle, M.-A. Félix | Nouragues Forest, French Guiana | 23 Nov 2009 | C. Braendle, M.-A. Félix | Japonica group | A few isolates from Nouragues, French Guiana | JU2083 | Richaud/Félix prepping DNA/RNA for Blaxter | |
yunquensis (ex-sp. 19) | EG6142 | F/M | S. Dalton | El Yunque, Puerto Rico | 28 Mar 2010 | S. Dalton, M. Ailion | Japonica group | Puerto Rico | |||
guadeloupensis (ex-sp. 20) | NIC113 | F/M | C. Braendle | Soufrière Forest trail, Guadeloupe | Mar 2010 | C. Braendle | Drosophilae supergroup | Guadeloupe | planned Braendle | ||
sp. 21 | NIC134 | F/M | C. Gimond | Island of Sainte Marie, Madagascar | Dec 2010 | C. Braendle | base of Caenorhabditis | Also Polynesia and Thailand (Félix) | planned Braendle | ||
latens (ex-sp. 23) | VX88 | F/M | G.-X. Wang | Jiufeng Village, Wuhan City, Hubei Province, China | 27 Oct 2009 | G.-X. Wang | Briggsae subgroup, sister of C. remanei | Several isolates from China (Cutter) | PX534, PX573, PX574, PX580 | under assembly, Cutter/Phillips | |
sp. 24 | QG555 | F/M | A. Paaby | Santa Barbara, USA | July 2011 | A. Paaby | Angaria group, sister of sp. 8 | 1 isolate from California and 3 from Panama (Rockman) | |||
sp. 25 | ZF1222 | F/M | A. Seah, T. Inoue | Singapore | 3 Sep 2011 | T. Inoue | Japonica group | 2 isolates from Singapore | ongoing (Inoue) | ||
sp. 26 | JU2161 | F/M | M.-A. Félix | Zanzibar, Tanzania | 9 Mar 2012 | M.-A. Félix | Briggsae subgroup, sister of sp. 5 | 5 isolates from Zanzibar | JU2190 | Blaxter, in process | |
sp. 27 | QX2263 | F/M | Buenos Aires, Argentina | 2 Mar 2012 | E. Andersen | Drosophilae supergroup, sister of sp. 6 | Argentina | ||||
sp. 28 | QG702 | F/M | M. Rockman | Barro Colorado Island, Panama | 23 Apr 2012 | M. Rockman | Japonica group | several isofemale lines from Panama | QG2080, QG2081 | under assembly, Rockman | |
sp. 29 | QG704 | F/M | M. Rockman | Barro Colorado Island, Panama | 25 Apr 2012 | M. Rockman | Japonica group, sister of sp. 17 | many isofemale lines from Panama | QG2082, QG2083 | planning Ailion, under assembly, Rockman | |
sp. 30 | DF5152 | F/M | Gallon Jug, Belize | 15 Nov 2012 | K. Kiontke | Drosophilae subgroup | 4 isofemale lines from Belize | ||||
sp. 31 | JU2469 | F/M | L. Frézal | Madre de Dios, Peru | Jan 2013 | L. Frézal | Drosophilae super group | 2 isolates from Peru | (lost) ongoing (Félix) | ||
sp. 32 | SB454 | F/M | East Africa? | Feb 2013 | W. Sudhaus | Japonica group, sister of sp. 7 | 1 isolate, from the gut of the millipede Archispirostreptus gigas | ongoing (Félix) | |||
sp. 33 | BRC20065 | F/M | J. Wang | Taiwan | 24 May 2012 | J. Wang | Briggsae subgroup | 1 isolate from Taiwan | BRC20066 | ||
sp. 34 | NK74SC | F/M | N. Kanzaki | Ishigaki Island, Japan | May 2013 | N. Kanzaki | "Elegans" supergroup | 1 isolate from Japan. Associated with fig wasps and Ficus septica | started by N. Kanzaki and collaborators | ||
sp. 35 | DF5171 | F/M | Banda Ache, Indonesia | Aug 2013 | N. Kanzaki | Elegans supergroup | 2 Isolates from Indonesia, associated with Ficus hispida | ||||
sp. 36 | NK02NV | F/M | N. Kanzaki | Tokyo, Japan | Apr 2013 | N. Kanzaki | Japonica group | 1 isolate from Japan. Associated with the weevil Niphades variegatus | |||
sp. 37 | NIC394 | F/M | C. Braendle, A. Cutter, R. Jovelin, N. Callemeyn | Nouragues National Reserve, French Guiana | 18 Apr 2013 | C. Braendle | Angaria group | 1 isolate from French Guiana |
Species numbers are assigned by Karin Kiontke, NYU.
Published phylogeny, up to sp. 21:
Published phylogeny from Kiontke et al. 2011 with species names from Félix, Braendle & Cutter 2014
Félix, Braendle @ Cutter PLoS One 2014 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0094723
Updated phylogeny, up to sp. 32: http://wormtails.bio.nyu.edu/RhabditinaDB_Images/GenusTrees/CaenorhabditisTree.png