Difference between revisions of "LIST OF AVAILABLE CAENORHABDITIS SPECIES and the state of their genome projects"
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| '''sp. 38''' || 38 || JU2745 || F/M || F. Besnard || Guadeloupe (Basse Terre) || 09 June 2014 || F. Besnard || ''Angaria'' group || 1 isolate from Guadeloupe || JU2809 || Blaxter, sequenced | | '''sp. 38''' || 38 || JU2745 || F/M || F. Besnard || Guadeloupe (Basse Terre) || 09 June 2014 || F. Besnard || ''Angaria'' group || 1 isolate from Guadeloupe || JU2809 || Blaxter, sequenced | ||
|- | |- | ||
− | | '''sp. 39''' || 39 || NIC564 || F/M || C. Braendle || Dominica || 13 May 2014 || C. Braendle || '' | + | | '''sp. 39''' || 39 || NIC564 || F/M || C. Braendle || Dominica || 13 May 2014 || C. Braendle || ''Japonica'' group || 1 isolate from Dominique || || Blaxter, sequenced |
|- | |- | ||
| '''sp. 40''' || 40 || JU2774 || F/M || J.-B. Pénigault || Danbulla, Australia || 08 August 2014 || L. Frézal || ''Briggsae'' subgroup, close relative of ''C. sinica'' || 5 isolates from Australia, in fresh or rotting figs || JU2818 || Blaxter, sequenced | | '''sp. 40''' || 40 || JU2774 || F/M || J.-B. Pénigault || Danbulla, Australia || 08 August 2014 || L. Frézal || ''Briggsae'' subgroup, close relative of ''C. sinica'' || 5 isolates from Australia, in fresh or rotting figs || JU2818 || Blaxter, sequenced | ||
|- | |- | ||
− | | '''sp. 41''' || 41 || BRC20276 || F/M || || Salomon Islands || October 2014 || J. Wang || ''Briggsae'' subgroup || 2 isolates from Salomon Islands || || | + | | '''sp. 41''' || 41 || BRC20276 || F/M || || Salomon Islands || October 2014 || J. Wang || ''Briggsae'' subgroup, sister species of C. sp. 40 || 2 isolates from Salomon Islands || || |
|- | |- | ||
− | | '''sp. 42''' || 42 || NIC1040 || F/M || C. Braendle/A. Cutter || Nouragues Forest, French Guiana || August 2014 || C. Braendle || | + | | '''sp. 42''' || 42 || NIC1040 || F/M || C. Braendle/A. Cutter || Nouragues Forest, French Guiana || August 2014 || C. Braendle || ''Drosophilae'' super group || one isolate from French Guiana || || |
|- | |- | ||
| '''sp. 43''' || 43 || NIC1070 || F/M || C. Gosse || Chichén Itzá, Yucatán, Mexico || 17 October 2014 || C. Braendle || ''Drosophilae'' super group || 2 isolates from Mexico; in orange berries || || Blaxter, sequenced | | '''sp. 43''' || 43 || NIC1070 || F/M || C. Gosse || Chichén Itzá, Yucatán, Mexico || 17 October 2014 || C. Braendle || ''Drosophilae'' super group || 2 isolates from Mexico; in orange berries || || Blaxter, sequenced | ||
|- | |- | ||
− | | '''sp. 44''' || 44 || BRC20300 || F/M || || Shihting mountain near Taipei City, Taiwan || Dec 2014 || J. Wang || | + | | '''sp. 44''' || 44 || BRC20300 || F/M || || Shihting mountain near Taipei City, Taiwan || Dec 2014 || J. Wang || sister species of ''C. brenneri'' || one isolate from Taiwan; in flowers || || |
|- | |- | ||
− | | '''sp. 45''' || 45 || NIC759 || F/M || C. Braendle || Sylvania, Dominica || 16 May 2014 ||C. Braendle || | + | | '''sp. 45''' || 45 || NIC759 || F/M || C. Braendle || Sylvania, Dominica || 16 May 2014 ||C. Braendle || sister species of ''C. guadeloupensis'' || one isolate from Dominica; in ''Cecropia'' fruit || |- |
+ | | '''sp. 46''' || 46 || NIC1120 || F/M || C. Braendle || Macchu Picchu, Aguas Calientes, Peru || 7 April 2015 ||C. Braendle || ''Japonica'' group || one isolate from Peru || || | ||
+ | |- | ||
+ | | '''sp. 47''' || 46 || NIC1127 || F/M || C. Braendle || Tambopata region, Amazon, Peru || 7 April 2015 ||C. Braendle || ''Angaria'' group || one isolate from Peru || || | ||
|} | |} |
Revision as of 15:10, 15 June 2015
4 Nov 2014: Great news: Mark Blaxter has obtained funding from Edinburgh Genomics to sequence 15-20 further species and launched the Caenorhabditis Genomes Project, see http://caenorhabditis.bio.ed.ac.uk/
Species name | species number | 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 | 3 | PS1010 | F/M | 1990 | Drosophilae super-group, Angaria group | 3 isolates from Florida USA | - | Mortazavi et al. 2010 Genome Research, @Wormbase | ||||||||||||||
brenneri | 4 | 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, sequenced. High proportion of bacterial DNA. To be reprepared in Felix lab. | ||||||||||||||||||
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 | 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 | 2 | DF5070 | F/M | S. Wirth | Corsica, France | Oct 2001 | W. Sudhaus | Drosophilae group, sister of C. drosophilae | 1 single isolate | |||||||||||||
sinica | 5 | 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 | 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 | 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 | 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) | ongoing using TGM13 (K. Kiontke) | ||||||||||||
nigoni | 9 | JU1325 | F/M | M.-A. Félix | Trivandrum Zoo, Kerala, India | 21 Dec 2007 | M.-A. Félix | Briggsae subgroup, sister of briggsae | Various wet tropical places from Yucatan to Singapore (Ailion, Félix, Inoue) | JU1422 | (Wash U: contaminated genomic, cDNAs OK) Resequenced by Barbara Meyer | |||||||||||
doughertyi | 10 | JU1333 | 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, sequenced, preliminary assembly; RNA seq for JU1328 & JU1333 http://www.ncbi.nlm.nih.gov/sra/?term=SRP042651+Caenorhabditis | |||||||||||
tropicalis | 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 | 12 | JU1426 | F/M | P. Châtelet | Nouragues Forest, French Guiana | May 2008 | M.-A. Félix | Angaria group | 2 isolates from French Guiana | JU1956 | Blaxter, sequenced | |||||||||||
virilis | 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 | Blaxter, sequenced | |||||||||||
imperialis | 14 | EG5716 | F/M | D. Ailion | Moorea, French Polynesia | 24 Jul 2009 | M. Ailion | Japonica group | also Polynesia, Guadeloupe (Félix, Braendle) | EG5942-EG5947 | ||||||||||||
kamaaina | 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 | 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 | 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 | Blaxter, sequenced | |||||||||||
macrosperma (ex-sp. 18) | 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 | Blaxter, sequenced | |||||||||||
yunquensis | 19 | EG6142 | F/M | S. Dalton | El Yunque, Puerto Rico | 28 Mar 2010 | S. Dalton, M. Ailion | Japonica group | Puerto Rico | |||||||||||||
guadeloupensis | 20 | NIC113 | F/M | C. Braendle | Soufrière Forest trail, Guadeloupe | Mar 2010 | C. Braendle | Drosophilae supergroup | Guadeloupe | Blaxter, sequenced | ||||||||||||
sp. 21 | 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 | Blaxter, sequenced | |||||||||||
latens | 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 | 24 | QG555 | F/M | A. Paaby | Santa Barbara, USA | July 2011 | A. Paaby | Angaria group, sister of sp. 8 | 1 isolate from California, 3 from Panama (Rockman), 1 from Mexico (Felix) | |||||||||||||
sp. 25 | 25 | ZF1222 | F/M | A. Seah, T. Inoue | Singapore | 3 Sep 2011 | T. Inoue | Japonica group | 2 isolates from Singapore | ongoing (Inoue) | ||||||||||||
sp. 26 | 26 | JU2161 | F/M | M.-A. Félix | Zanzibar, Tanzania | 9 Mar 2012 | M.-A. Félix | Briggsae subgroup, close relative of C. sinica | 5 isolates from Zanzibar | JU2190 | Blaxter, sequenced | |||||||||||
sp. 27 | 27 | QX2263 | F/M | Buenos Aires, Argentina | 2 Mar 2012 | E. Andersen | Drosophilae supergroup, sister of portoensis | Argentina | ||||||||||||||
sp. 28 | 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 | 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 | 30 | DF5152 | F/M | Gallon Jug, Belize | 15 Nov 2012 | K. Kiontke | Drosophilae subgroup | 4 isofemale lines from Belize | ongoing (K. Kiontke) | |||||||||||||
sp. 31 | 31 | JU2469 | F/M | Madre de Dios, Peru | Jan 2013 | L. Frézal | Drosophilae super group | 2 isolates from Peru | JU2585 | Blaxter, sequenced | ||||||||||||
sp. 32 | 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 | Blaxter, in sequencing queue | ||||||||||||
sp. 33 | 33 | BRC20065 | F/M | J. Wang | Taiwan | 24 May 2012 | J. Wang | Briggsae subgroup | 1 isolate from Taiwan | BRC20066 | planned by J. Wang | |||||||||||
sp. 34 | 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 | 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 | 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 | 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 | 38 | JU2745 | F/M | F. Besnard | Guadeloupe (Basse Terre) | 09 June 2014 | F. Besnard | Angaria group | 1 isolate from Guadeloupe | JU2809 | Blaxter, sequenced | |||||||||||
sp. 39 | 39 | NIC564 | F/M | C. Braendle | Dominica | 13 May 2014 | C. Braendle | Japonica group | 1 isolate from Dominique | Blaxter, sequenced | ||||||||||||
sp. 40 | 40 | JU2774 | F/M | J.-B. Pénigault | Danbulla, Australia | 08 August 2014 | L. Frézal | Briggsae subgroup, close relative of C. sinica | 5 isolates from Australia, in fresh or rotting figs | JU2818 | Blaxter, sequenced | |||||||||||
sp. 41 | 41 | BRC20276 | F/M | Salomon Islands | October 2014 | J. Wang | Briggsae subgroup, sister species of C. sp. 40 | 2 isolates from Salomon Islands | ||||||||||||||
sp. 42 | 42 | NIC1040 | F/M | C. Braendle/A. Cutter | Nouragues Forest, French Guiana | August 2014 | C. Braendle | Drosophilae super group | one isolate from French Guiana | |||||||||||||
sp. 43 | 43 | NIC1070 | F/M | C. Gosse | Chichén Itzá, Yucatán, Mexico | 17 October 2014 | C. Braendle | Drosophilae super group | 2 isolates from Mexico; in orange berries | Blaxter, sequenced | ||||||||||||
sp. 44 | 44 | BRC20300 | F/M | Shihting mountain near Taipei City, Taiwan | Dec 2014 | J. Wang | sister species of C. brenneri | one isolate from Taiwan; in flowers | ||||||||||||||
sp. 45 | 45 | NIC759 | F/M | C. Braendle | Sylvania, Dominica | 16 May 2014 | C. Braendle | sister species of C. guadeloupensis | one isolate from Dominica; in Cecropia fruit | - | sp. 46 | 46 | NIC1120 | F/M | C. Braendle | Macchu Picchu, Aguas Calientes, Peru | 7 April 2015 | C. Braendle | Japonica group | one isolate from Peru | ||
sp. 47 | 46 | NIC1127 | F/M | C. Braendle | Tambopata region, Amazon, Peru | 7 April 2015 | C. Braendle | Angaria group | one isolate from Peru |
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