Difference between revisions of "LIST OF AVAILABLE CAENORHABDITIS SPECIES and the state of their genome projects"
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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''' | ||
|- | |- | ||
| − | | '''''brenneri''''' || || F/M || || || || || ''Elegans'' group ||tropical, ~30 isolates (Felix, Cutter, Braendle) || PB2801, VX223-225, VX227 || Wash U, '''@Wormbase'''; VX strains sequenced but not yet assembled (Cutter lab) | + | | '''''brenneri''''' || || F/M || || || || || ''Elegans'' group ||tropical, ~30 isolates (Felix, Cutter, Braendle) || PB2801, VX223-225, VX227 || Wash U, '''@Wormbase'''; VX strains sequenced but not yet assembled (Cutter lab); RNA seq for 10 isolates http://www.ncbi.nlm.nih.gov/sra/?term=SRP042651+Caenorhabditis |
|- | |- | ||
| '''''briggsae''''' || AF16 || '''H/M''' || || || || || ''Elegans'' group || world-wide distribution, 100s of isolates || N.A. || Stein et al. 2003 PLoS Biology, '''@Wormbase'''; 37 wild isolates sequenced 30x (Cutter lab) | | '''''briggsae''''' || AF16 || '''H/M''' || || || || || ''Elegans'' group || world-wide distribution, 100s of isolates || N.A. || Stein et al. 2003 PLoS Biology, '''@Wormbase'''; 37 wild isolates sequenced 30x (Cutter lab) | ||
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|'''''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 | |'''''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 | + | |'''''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; RNA seq for JU1328 & JU1333 http://www.ncbi.nlm.nih.gov/sra/?term=SRP042651+Caenorhabditis |
|- | |- | ||
| '''''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''' | | '''''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''' | ||
Revision as of 11:39, 4 October 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, VX223-225, VX227 | Wash U, @Wormbase; VX strains sequenced but not yet assembled (Cutter lab); RNA seq for 10 isolates http://www.ncbi.nlm.nih.gov/sra/?term=SRP042651+Caenorhabditis | ||||||
| briggsae | AF16 | H/M | Elegans group | world-wide distribution, 100s of isolates | N.A. | Stein et al. 2003 PLoS Biology, @Wormbase; 37 wild isolates sequenced 30x (Cutter lab) | |||||
| 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, PX356, PX349 | Wash U, @Wormbase; PX strains sequenced and assembled (ms in review, Phillips/Cutter labs); approx 35 wild isolates sequenced | ||||||
| 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; RNA seq for JU1328 & JU1333 http://www.ncbi.nlm.nih.gov/sra/?term=SRP042651+Caenorhabditis | |
| 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, Thailand and Caribbean (Félix) | NIC534 | ||
| 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 portoensis | 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 nouraguensis | 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 | Madre de Dios, Peru | Jan 2013 | L. Frézal | Drosophilae super group | 2 isolates from Peru | JU2585 | Richaud/Félix prepping DNA/RNA for Blaxter | ||
| sp. 32 | SB454 | F/M | East Africa? | Feb 2013 | W. Sudhaus | Japonica group, sister of afra | 1 isolate, from the gut of the millipede Archispirostreptus gigas | JU2788 | Richaud/Félix prepping DNA/RNA for Blaxter | ||
| sp. 33 | BRC20065 | F/M | J. Wang | Taiwan | 24 May 2012 | J. Wang | Briggsae subgroup | 1 isolate from Taiwan | BRC20066 | Richaud/Félix prepping DNA/RNA for Blaxter | |
| sp. 34 | NK74SC | F/M | N. Kanzaki | Ishigaki Island, Japan | May 2013 | N. Kanzaki | Elegans supergroup, with C. sp. 35 sister of C. elegans | 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, with C. sp. 34 sister of C. elegans | 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 | |||
| sp. 38 | JU2745 | F/M | F. Besnard | Guadeloupe (Basse Terre) | 09 June 2014 | F. Besnard | Angaria group | 1 isolate from Guadeloupe | ongoing (Félix lab) | ||
| sp. 39 | NIC564 | F/M | C. Braendle | Dominica | 13 May 2014 | C. Braendle | Angaria group | 1 isolate from Dominique | |||
| sp. 40 | JU2774 | F/M | J.-B. Pénigault | Danbulla, Australia | 08 August 2014 | L. Frézal | Briggsae subgroup, close relative of C. sp. 5 | 5 isolates from Australia, in fresh or rotting figs | ongoing (Félix lab) |
Species numbers are assigned by Karin Kiontke, NYU.
Published phylogeny, up to sp. 21:
Kiontke et al. 2011 BMC Evolutionary Biology 11: 339.
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
