Difference between revisions of "LIST OF AVAILABLE CAENORHABDITIS SPECIES and the state of their genome projects"
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+ | See [https://wormtails.bio.nyu.edu/fmi/webd/RhabditinaDB?homeurl=http://wormtails.bio.nyu.edu/Databases.html RhabditinaDB] for a comprehensive morphological and taxonomic database of Rhabditina, including ''Caenorhabditis'' | ||
+ | |||
{| class="wikitable" | {| class="wikitable" | ||
− | |||
|- | |- | ||
− | ! Species | + | ! Species !! number !! Reference strain !! Repro- duction !! Collector !! Location !! Date !! Isolated by !! Supergroup (annotation incomplete) !! Group (annotation incomplete) !! Geographic distribution and available isolates (lab) !! Inbred strain !! Genome !! Data ([http://wormbase.org WORMBASE] or other) !! Publications (incomplete) !! Other strains sequenced & other sequence data |
+ | |- | ||
+ | | elegans || a || N2 || H/M || - || - || - || - || Elegans || || world-wide (mostly temperate) distribution, 100s of isolates || N.A. || SEQUENCED Sanger WashU || [http://wormbase.org WORMBASE] || C. elegans Sequencing Consortium 1998 Science || >400 wild isolates sequenced, see [https://www.elegansvariation.org/ CeNDR] | ||
+ | |- | ||
+ | | briggsae || b || AF16 || H/M || - || - || - || - || Elegans || || world-wide distribution, 100s of isolates || N.A. || SEQUENCED WashU || [http://wormbase.org WORMBASE] || [https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0000045 Stein et al. 2003] || 37 wild isolates sequenced 30x (Cutter lab) | ||
+ | |- | ||
+ | | japonica || c || || F/M || - || - || - || - || Elegans || Japonica || isolates from Japan (Yoshiga/Cutter) || DF5080 || SEQUENCED WashU || [http://wormbase.org WORMBASE] || - || - | ||
+ | |- | ||
+ | | remanei || d || || F/M || - || - || - || - || Elegans || || USA/Canada, Europe, Japan, Taiwan, 100s of isolates || PB4641, PX356, PX349 || SEQUENCED WashU, Phillips || [http://wormbase.org WORMBASE] || [https://doi.org/10.1371/journal.pgen.1005323 Fierst et al. 2015] || approx 35 wild isolates sequenced | ||
+ | |- | ||
+ | | drosophilae || f || DF5077 || F/M || - || - || - || - || Drosophilae || || rotting saguaro cactus in Arizona, a few isolates || DF5112 || IN SEQUENCING Blaxter || - || - || - | ||
+ | |- | ||
+ | | plicata || g || SB355 || F/M || - || - || - || - || base || || - || - || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || - | ||
+ | |- | ||
+ | | monodelphis || 1 || SB341 || F/M || J. Raschka || Berlin, Germany || 2001 || W. Sudhaus || base || || A second isolate from Norway (Félix) || JU1667 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://bmczool.biomedcentral.com/articles/10.1186/s40850-017-0013-2 Slos et al. BMC Zool. 2017] || - | ||
+ | |- | ||
+ | | sp. 2 || 2 || DF5070 || F/M || S. Wirth || Corsica, France || Oct 2001 || W. Sudhaus || Drosophilae || (sister of drosophilae) || 1 single isolate || - || IN SEQUENCING Blaxter || - || - || - | ||
+ | |- | ||
+ | | angaria || 3 || PS1010 || F/M || - || - || 1990 || - || Drosophilae || Angaria || 3 isolates from Florida USA || - || SEQUENCED CalTech || [http://wormbase.org WORMBASE] || [https://doi.org/10.1101/gr.111021.110 Mortazavi et al.] || - | ||
|- | |- | ||
− | | | + | | brenneri || 4 || || F/M || - || - || - || - || Elegans || Elegans || tropical, ~30 isolates (Felix, Cutter, Braendle) || PB2801, VX223-225, VX227 || SEQUENCED WashU || [http://wormbase.org 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 |
|- | |- | ||
− | | | + | | sinica || 5 || || F/M || M.-A. Félix || Chengyang, Guangxi, China || 6 May 2005 || M.-A. Félix || Elegans || Briggase || Isolates from China, Vietnam (Cutter, Ailion, Félix) || JU800 || SEQUENCED Cutter Blaxter || [http://wormbase.org 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 || Sequencing_planned Blaxter || - || - || - |
|- | |- | ||
− | | | + | | afra || 7 || JU1199 || F/M || M. Herrmann || Begoro, Ghana || Jun 2007 || M.-A. Félix || Japonica group || Japonica || 2 isolates from West Africa (Félix) || JU1286 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || - |
− | | | ||
− | | | ||
|- | |- | ||
− | | | + | | sp. 8 || 8 || QX1182 || F/M || M. Rockman || Backyard of 93 Mercer St., Jersey City, NJ, USA || 28 Jul 2007 || M. Rockman || Angaria group || Angaria || Isolates from USA (Fitch), Europe (Braendle, Félix), Canada (Rockman) || JU3312 || IN SEQUENCING Blaxter || - || - || - |
|- | |- | ||
− | | | + | | nigoni || 9 || JU1325 || F/M || M.-A. Félix || Trivandrum Zoo, Kerala, India || 21 Dec 2007 || M.-A. Félix || Briggsae subgroup, sister of briggsae || Briggsae || Various wet tropical places from Yucatan to Singapore (Ailion, Félix, Inoue) || JU1422 || SEQUENCED Schwarz || [https://doi.org/10.17605/osf.io/dkbwt OPEN SCIENCE FRAMEWORK] || - || - |
|- | |- | ||
− | | | + | | doughertyi || 10 || JU1333 || F/M || M.-A. Félix || Angela Spice Garden, Kerala, India || 27 Dec 2007 || M.-A. Félix || Brenneri subgroup || Brenneri || 6 isolates from South India || JU1771 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || RNA seq for JU1328 & JU1333 |
|- | |- | ||
− | | | + | | tropicalis || 11 || JU1373 || H/M || V. Robert, L. Sablé || Saint-Benoît, La Réunion || Jan 2008 || M.-A. Félix || Brenneri subgroup || Brenneri || Common in tropical regions (not so far on the African continent, one in Asia) || - || SEQUENCED WashU || [http://wormbase.org WORMBASE] || - || - |
|- | |- | ||
− | | | + | | castelli || 12 || JU1426 || F/M || P. Châtelet || Nouragues Forest, French Guiana || May 2008 || M.-A. Félix || Angaria group || Angaria || Several isolates from French Guiana (Félix, Braendle, Cutter) || JU1956 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || - |
|- | |- | ||
− | | | + | | virilis || 13 || JU1528 || F/M || M.-A. Félix || Orsay apple orchard || 9 Sep 2008 || M.-A. Félix || Drosophilae super group || || Several isolates from two locations in France || JU1968 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || - |
|- | |- | ||
− | | | + | | imperialis || 14 || EG5716 || F/M || D. Ailion || Moorea, French Polynesia || 24 Jul 2009 || M. Ailion || Japonica group || || also Polynesia, Guadeloupe (Félix, Braendle) || EG5942-EG5947 || IN SEQUENCING Blaxter || - || - || - |
|- | |- | ||
− | | | + | | 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 || SEQUENCED Rockman || [http://caenorhabditis.org Caenorhabditis DB] || - || |
|- | |- | ||
− | | | + | | 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 || in assembly Schwarz || || - || |
|- | |- | ||
− | | | + | | 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 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || additional strains sequenced |
|- | |- | ||
− | | | + | | macrosperma || 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 || SEQUENCED Cutter || [http://caenorhabditis.org Caenorhabditis DB] || - || - |
|- | |- | ||
− | | | + | | yunquensis || 19 || EG6142 || F/M || S. Dalton || El Yunque, Puerto Rico || 28 Mar 2010 || S. Dalton, M. Ailion || Japonica group || || Puerto Rico || XZ1517-XZ1520 || IN SEQUENCING Blaxter || - || - || - |
|- | |- | ||
− | | | + | | guadeloupensis || 20 || NIC113 || F/M || C. Braendle || Soufrière Forest trail, Guadeloupe || Mar 2010 || C. Braendle || Drosophilae supergroup || || Guadeloupe || || SEQUENCED_draft Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || resequencing required |
|- | |- | ||
− | | | + | | parvicauda || 21 || NIC134 || F/M || C. Gimond || Island of Sainte Marie, Madagascar || Dec 2010 || C. Braendle || base || || Also Polynesia, Thailand and Caribbean (Félix) || NIC534 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://doi.org/10.1101/398446, BIORXIV] || - |
|- | |- | ||
− | | | + | | 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 || SEQUENCED Phillips || [http://caenorhabditis.org Caenorhabditis DB] || - || - |
|- | |- | ||
− | | | + | | sp. 24 || 24 || QG555 || F/M || A. Paaby || Santa Barbara, USA || July 2011 || A. Paaby || Angaria group, sister of sp. 8 || Angaria || Isolates from California, Panama, Mexico (Rockman, Félix) || || IN SEQUENCING Blaxter || - || - || - |
|- | |- | ||
− | | | + | | sp. 25 || 25 || ZF1222 || F/M || A. Seah, T. Inoue || Singapore || 3 Sep 2011 || T. Inoue || Japonica group || Japonica || 2 isolates from Singapore || ZF1457 || IN SEQUENCING Blaxter || - || - || - |
|- | |- | ||
− | | | + | | zanzibari || 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 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://doi.org/10.1101/398446, BIORXIV] || - |
|- | |- | ||
− | | | + | | sp. 27 || 27 || QX2263 || F/M || - || Buenos Aires, Argentina || 2 Mar 2012 || E. Andersen || Drosophilae supergroup, sister of portoensis || || Argentina || || IN SEQUENCING Blaxter || - || - || - |
|- | |- | ||
− | | | + | | panamensis || 28 || QG702 || F/M || M. Rockman || Barro Colorado Island, Panama || 23 Apr 2012 || M. Rockman || Japonica group || Japonica || several isofemale lines from Panama || QG2080, QG2081 || SEQUENCED Rockman || [http://caenorhabditis.org Caenorhabditis DB] || [https://doi.org/10.1101/398446, BIORXIV] || - |
|- | |- | ||
− | | | + | | becei || 29 || QG704 || F/M || M. Rockman || Barro Colorado Island, Panama || 25 Apr 2012 || M. Rockman || Japonica group, sister of nouraguensis || Japonica || many isofemale lines from Panama || QG2082, QG2083 || SEQUENCED Rockman || [http://caenorhabditis.org Caenorhabditis DB] || [https://doi.org/10.1101/398446, BIORXIV] || - |
|- | |- | ||
− | | | + | | sp. 30 || 30 || DF5152 || F/M || - || Gallon Jug, Belize || 15 Nov 2012 || K. Kiontke || Drosophilae subgroup || || 4 isofemale lines from Belize || ongoing (K. Kiontke) || IN SEQUENCING Blaxter || - || - || - |
|- | |- | ||
− | | | + | | uteleia || 31 || JU2469 || F/M || - || Madre de Dios, Peru || Jan 2013 || L. Frézal || May branch basally within the Elegans supergroup, see Slos et al. || || 2 isolates from Peru || JU2585 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://doi.org/10.1101/398446, BIORXIV] || - |
|- | |- | ||
− | | | + | | sulstoni || 32 || SB454 || F/M || - || East Africa? || Feb 2013 || W. Sudhaus || Japonica group, sister of afra || Japonica || 1 isolate, from the gut of the millipede Archispirostreptus gigas || JU2788 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://doi.org/10.1101/398446, BIORXIV] || - |
|- | |- | ||
− | | | + | | sp. 33 || 33 || BRC20065 || F/M || J. Wang || Taiwan || 24 May 2012 || J. Wang || Elegans || Briggsae || 1 isolate from Taiwan || BRC20066 || IN SEQUENCING Wang Tsai || - || - || - |
|- | |- | ||
− | | | + | | inopinata || 34 || NK74SC || F/M || N. Kanzaki || Shigaki Island, Japan || May 2013 || N. Kanzaki || Elegans || Elegans supergroup, with C. sp. 35 sister of C. elegans || 1 isolate from Japan. Associated with fig wasps and Ficus septica || - || SEQUENCED Kanzaki, Kikuchi || [http://caenorhabditis.org Caenorhabditis DB] || - || - |
|- | |- | ||
− | | | + | | 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 || - || IN SEQUENCING Kanzaki, Kikuchi || - || - || - |
|- | |- | ||
− | | | + | | sp. 36 || 36 || NK02NV || F/M || N. Kanzaki || Tokyo, Japan || Apr 2013 || N. Kanzaki || Japonica group || Japonica || 1 isolate from Japan. Associated with the weevil Niphades variegatus || - || IN SEQUENCING Kanzaki, Kikuchi || - || - || - |
|- | |- | ||
− | | | + | | 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 || Angaria || 1 isolate from French Guiana || - || IN SEQUENCING Blaxter || - || - || - |
|- | |- | ||
− | | | + | | quiockensis || 38 || JU2745 || F/M || F. Besnard || Guadeloupe (Basse Terre) || 09 June 2014 || F. Besnard || Angaria group || Angaria || 1 isolate from Guadeloupe || JU2809 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://doi.org/10.1101/398446, BIORXIV] || - |
|- | |- | ||
− | || | + | | waitukubuli || 39 || NIC564 || F/M || C. Braendle || Dominica || 13 May 2014 || C. Braendle || Japonica group || Japonica || 1 isolate from Dominique || - || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://doi.org/10.1101/398446, BIORXIV] || - |
|- | |- | ||
− | | | + | | tribulationis || 40 || JU2774 || F/M || J.-B. Pénigault || Danbulla, Australia || 08 August 2014 || L. Frézal || Briggsae subgroup, close relative of C. sinica || Briggsae || 5 isolates from Australia, in fresh or rotting figs || JU2818 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://doi.org/10.1101/398446, BIORXIV] || - |
|- | |- | ||
− | | | + | | sp. 41 || 41 || BRC20276 || F/M || - || Solomon Islands || October 2014 || J. Wang || Briggsae subgroup, sister species of C. sp. 40 || Briggsae || 2 isolates from Solomon Islands || - || IN SEQUENCING Wang Tsai || - || - || - |
|- | |- | ||
− | | | + | | sp. 42 || 42 || NIC1040 || F/M || C. Braendle/A. Cutter || Nouragues Forest, French Guiana || August 2014 || C. Braendle || Drosophilae super group || Drosophilae || one isolate from French Guiana || - || IN SEQUENCING Blaxter || - || - || - |
|- | |- | ||
− | | | + | | vivipara || 43 || NIC1070 || F/M || C. Gosse || Chichén Itzá, Yucatán, Mexico || 17 October 2014 || C. Braendle || Drosophilae super group || Drsophilae || 2 isolates from Mexico; in orange berries || NIC1581 || SEQUENCED_draft Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://doi.org/10.1101/398446, BIORXIV] || resequencing required |
|- | |- | ||
− | | | + | | sp. 44 || 44 || BRC20300 || F/M || J. Wang || Shihting mountain near Taipei City, Taiwan || Dec 2014 || J. Wang || sister species of C. brenneri || || one isolate from Taiwan; in flowers || - || IN SEQUENCING Wang Tsai || - || - || - |
|- | |- | ||
− | | | + | | 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 || - || IN SEQUENCING Blaxter || - || - || - |
|- | |- | ||
− | | | + | | sp. 46 || 46 || NIC1120 || F/M || C. Braendle || Macchu Picchu, Aguas Calientes, Peru || 7 April 2015 || C. Braendle || Japonica group || Japonica || one isolate from Peru || - || Sequencing_planned Blaxter || - || - || - |
|- | |- | ||
− | | | + | | sp. 47 || 47 || NIC1127 || F/M || C. Braendle || Tambopata region, Amazon, Peru || 7 April 2015 || C. Braendle || Angaria group || Angaria || one isolate from Peru || - || Sequencing_planned Blaxter || - || - || - |
|- | |- | ||
− | | | + | | sp. 48 || 48 || BRC20359 || F/M || J. Wang || Khao Yai National park, Thailand || 4 May 2015 || J. Wang || sister of C. brenneri || Brenneri || one isolate from Thailand || - || Sequencing_planned Blaxter || - || - || - |
|- | |- | ||
− | | | + | | sp. 49 || 49 || BRC20376 || F/M || J. Wang || Solomon Islands || - || J. Wang || Japonica group? || Japonica || one isolate Solomon Islands || - || Sequencing_planned Blaxter || - || - || - |
|- | |- | ||
− | | | + | | sp. 50 || 50 || BRC20387 || F/M || Dai || near Taipei City, Taiwan || 18 October 2015 ||J. Wang || Elegans || Elegans || two isolates from Taiwan || - || Sequencing_planned Blaxter || - || - || - |
|- | |- | ||
− | | | + | | sp. 51 || 51 || QG2915 || F/M || M. Rockman || Australia || 2017 || M Rockman || Elegans || Elegans || one isolate from Australia || - || Sequencing_planned Blaxter || - || - || - |
|- | |- | ||
− | | | + | | sp. 52 || 52 || QG2933 || F/M || M. Rockman || Australia || 2017 || M Rockman || Drosophilae || || one isolate from Australia || - || Sequencing_planned Blaxter || - || - || - |
|- | |- | ||
− | | | + | | sp. 53 || 53 || ECA821 || F/M || E. Andersen || Oahu, Hawaii || 2017 || T Crombie || sister of C. kamaaina || || several isolates from Oahu and Kauai || - || Sequencing_planned Blaxter || - || - || - |
|- | |- | ||
− | | | + | | sp. 54 || 54 || BRC20468 || F/M || Hsueh, Yen-Ping || Miaoli County?, Taiwan || 18 August 2016 || J Wang || Elegans || || || - || Sequencing_planned Blaxter || - || - || - |
+ | |- | ||
+ | | sp. 55 || 55 || JU3317 || F/M || M.-A. Félix || Pugao Laozhai, Yuanyang, Yunnan, China || 5 March 2018 || M.-A. Félix || Elegans || || one isolate from Yunnan, China || - || Sequencing_planned Blaxter || - || - || - | ||
+ | |- | ||
+ | | sp. 56 || 56 || JU2215 || F/M || M. Joron || Tarapoto, Peru || October 2012 || L. Frézal || Angaria group, close to spp. 8 and 24 || Angaria || one isolate from Peru || (JU3313 8x inbred and very sick) || Sequencing_planned Blaxter || - || - || - | ||
+ | |- | ||
+ | | sp. 57 || 57 || QG3050 || F/M || M. Rockman || Barro Colorado Island, Panama || August 2018 || M. Rockman || near monodelphis and sonorae? || || two isolates from Panama || in inbreeding || || - || - || - | ||
|- | |- | ||
− | |||
− | |||
|} | |} | ||
Line 123: | Line 144: | ||
</gallery> | </gallery> | ||
'''Updated phylogeny, up to sp. 32:''' | '''Updated phylogeny, up to sp. 32:''' | ||
+ | |||
http://wormtails.bio.nyu.edu/RhabditinaDB_Images/GenusTrees/CaenorhabditisTree.png | http://wormtails.bio.nyu.edu/RhabditinaDB_Images/GenusTrees/CaenorhabditisTree.png | ||
+ | |||
+ | |||
+ | '''2017 phylogeny of a subset of species, based on their genome sequences by Slos et al.''' | ||
+ | |||
+ | https://bmczool.biomedcentral.com/articles/10.1186/s40850-017-0013-2 | ||
+ | |||
+ | '''See also''' | ||
+ | [https://doi.org/10.1101/398446, BIORXIV] |
Revision as of 11:38, 17 December 2018
See RhabditinaDB for a comprehensive morphological and taxonomic database of Rhabditina, including Caenorhabditis
Species | number | Reference strain | Repro- duction | Collector | Location | Date | Isolated by | Supergroup (annotation incomplete) | Group (annotation incomplete) | Geographic distribution and available isolates (lab) | Inbred strain | Genome | Data (WORMBASE or other) | Publications (incomplete) | Other strains sequenced & other sequence data |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
elegans | a | N2 | H/M | - | - | - | - | Elegans | world-wide (mostly temperate) distribution, 100s of isolates | N.A. | SEQUENCED Sanger WashU | WORMBASE | C. elegans Sequencing Consortium 1998 Science | >400 wild isolates sequenced, see CeNDR | |
briggsae | b | AF16 | H/M | - | - | - | - | Elegans | world-wide distribution, 100s of isolates | N.A. | SEQUENCED WashU | WORMBASE | Stein et al. 2003 | 37 wild isolates sequenced 30x (Cutter lab) | |
japonica | c | F/M | - | - | - | - | Elegans | Japonica | isolates from Japan (Yoshiga/Cutter) | DF5080 | SEQUENCED WashU | WORMBASE | - | - | |
remanei | d | F/M | - | - | - | - | Elegans | USA/Canada, Europe, Japan, Taiwan, 100s of isolates | PB4641, PX356, PX349 | SEQUENCED WashU, Phillips | WORMBASE | Fierst et al. 2015 | approx 35 wild isolates sequenced | ||
drosophilae | f | DF5077 | F/M | - | - | - | - | Drosophilae | rotting saguaro cactus in Arizona, a few isolates | DF5112 | IN SEQUENCING Blaxter | - | - | - | |
plicata | g | SB355 | F/M | - | - | - | - | base | - | - | SEQUENCED Blaxter | Caenorhabditis DB | - | - | |
monodelphis | 1 | SB341 | F/M | J. Raschka | Berlin, Germany | 2001 | W. Sudhaus | base | A second isolate from Norway (Félix) | JU1667 | SEQUENCED Blaxter | Caenorhabditis DB | Slos et al. BMC Zool. 2017 | - | |
sp. 2 | 2 | DF5070 | F/M | S. Wirth | Corsica, France | Oct 2001 | W. Sudhaus | Drosophilae | (sister of drosophilae) | 1 single isolate | - | IN SEQUENCING Blaxter | - | - | - |
angaria | 3 | PS1010 | F/M | - | - | 1990 | - | Drosophilae | Angaria | 3 isolates from Florida USA | - | SEQUENCED CalTech | WORMBASE | Mortazavi et al. | - |
brenneri | 4 | F/M | - | - | - | - | Elegans | Elegans | tropical, ~30 isolates (Felix, Cutter, Braendle) | PB2801, VX223-225, VX227 | SEQUENCED WashU | 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 | |
sinica | 5 | F/M | M.-A. Félix | Chengyang, Guangxi, China | 6 May 2005 | M.-A. Félix | Elegans | Briggase | Isolates from China, Vietnam (Cutter, Ailion, Félix) | JU800 | SEQUENCED 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 | Sequencing_planned Blaxter | - | - | - | |
afra | 7 | JU1199 | F/M | M. Herrmann | Begoro, Ghana | Jun 2007 | M.-A. Félix | Japonica group | Japonica | 2 isolates from West Africa (Félix) | JU1286 | SEQUENCED Blaxter | Caenorhabditis DB | - | - |
sp. 8 | 8 | QX1182 | F/M | M. Rockman | Backyard of 93 Mercer St., Jersey City, NJ, USA | 28 Jul 2007 | M. Rockman | Angaria group | Angaria | Isolates from USA (Fitch), Europe (Braendle, Félix), Canada (Rockman) | JU3312 | IN SEQUENCING Blaxter | - | - | - |
nigoni | 9 | JU1325 | F/M | M.-A. Félix | Trivandrum Zoo, Kerala, India | 21 Dec 2007 | M.-A. Félix | Briggsae subgroup, sister of briggsae | Briggsae | Various wet tropical places from Yucatan to Singapore (Ailion, Félix, Inoue) | JU1422 | SEQUENCED Schwarz | OPEN SCIENCE FRAMEWORK | - | - |
doughertyi | 10 | JU1333 | F/M | M.-A. Félix | Angela Spice Garden, Kerala, India | 27 Dec 2007 | M.-A. Félix | Brenneri subgroup | Brenneri | 6 isolates from South India | JU1771 | SEQUENCED Blaxter | Caenorhabditis DB | - | RNA seq for JU1328 & JU1333 |
tropicalis | 11 | JU1373 | H/M | V. Robert, L. Sablé | Saint-Benoît, La Réunion | Jan 2008 | M.-A. Félix | Brenneri subgroup | Brenneri | Common in tropical regions (not so far on the African continent, one in Asia) | - | SEQUENCED WashU | WORMBASE | - | - |
castelli | 12 | JU1426 | F/M | P. Châtelet | Nouragues Forest, French Guiana | May 2008 | M.-A. Félix | Angaria group | Angaria | Several isolates from French Guiana (Félix, Braendle, Cutter) | JU1956 | SEQUENCED Blaxter | Caenorhabditis DB | - | - |
virilis | 13 | JU1528 | F/M | M.-A. Félix | Orsay apple orchard | 9 Sep 2008 | M.-A. Félix | Drosophilae super group | Several isolates from two locations in France | JU1968 | SEQUENCED Blaxter | Caenorhabditis DB | - | - | |
imperialis | 14 | EG5716 | F/M | D. Ailion | Moorea, French Polynesia | 24 Jul 2009 | M. Ailion | Japonica group | also Polynesia, Guadeloupe (Félix, Braendle) | EG5942-EG5947 | IN SEQUENCING Blaxter | - | - | - | |
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 | SEQUENCED Rockman | Caenorhabditis DB | - | ||
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 | in assembly Schwarz | - | |||
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 | SEQUENCED Blaxter | Caenorhabditis DB | - | additional strains sequenced | |
macrosperma | 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 | SEQUENCED Cutter | Caenorhabditis DB | - | - | |
yunquensis | 19 | EG6142 | F/M | S. Dalton | El Yunque, Puerto Rico | 28 Mar 2010 | S. Dalton, M. Ailion | Japonica group | Puerto Rico | XZ1517-XZ1520 | IN SEQUENCING Blaxter | - | - | - | |
guadeloupensis | 20 | NIC113 | F/M | C. Braendle | Soufrière Forest trail, Guadeloupe | Mar 2010 | C. Braendle | Drosophilae supergroup | Guadeloupe | SEQUENCED_draft Blaxter | Caenorhabditis DB | - | resequencing required | ||
parvicauda | 21 | NIC134 | F/M | C. Gimond | Island of Sainte Marie, Madagascar | Dec 2010 | C. Braendle | base | Also Polynesia, Thailand and Caribbean (Félix) | NIC534 | SEQUENCED Blaxter | Caenorhabditis DB | BIORXIV | - | |
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 | SEQUENCED Phillips | Caenorhabditis DB | - | - | |
sp. 24 | 24 | QG555 | F/M | A. Paaby | Santa Barbara, USA | July 2011 | A. Paaby | Angaria group, sister of sp. 8 | Angaria | Isolates from California, Panama, Mexico (Rockman, Félix) | IN SEQUENCING Blaxter | - | - | - | |
sp. 25 | 25 | ZF1222 | F/M | A. Seah, T. Inoue | Singapore | 3 Sep 2011 | T. Inoue | Japonica group | Japonica | 2 isolates from Singapore | ZF1457 | IN SEQUENCING Blaxter | - | - | - |
zanzibari | 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 | SEQUENCED Blaxter | Caenorhabditis DB | BIORXIV | - | |
sp. 27 | 27 | QX2263 | F/M | - | Buenos Aires, Argentina | 2 Mar 2012 | E. Andersen | Drosophilae supergroup, sister of portoensis | Argentina | IN SEQUENCING Blaxter | - | - | - | ||
panamensis | 28 | QG702 | F/M | M. Rockman | Barro Colorado Island, Panama | 23 Apr 2012 | M. Rockman | Japonica group | Japonica | several isofemale lines from Panama | QG2080, QG2081 | SEQUENCED Rockman | Caenorhabditis DB | BIORXIV | - |
becei | 29 | QG704 | F/M | M. Rockman | Barro Colorado Island, Panama | 25 Apr 2012 | M. Rockman | Japonica group, sister of nouraguensis | Japonica | many isofemale lines from Panama | QG2082, QG2083 | SEQUENCED Rockman | Caenorhabditis DB | BIORXIV | - |
sp. 30 | 30 | DF5152 | F/M | - | Gallon Jug, Belize | 15 Nov 2012 | K. Kiontke | Drosophilae subgroup | 4 isofemale lines from Belize | ongoing (K. Kiontke) | IN SEQUENCING Blaxter | - | - | - | |
uteleia | 31 | JU2469 | F/M | - | Madre de Dios, Peru | Jan 2013 | L. Frézal | May branch basally within the Elegans supergroup, see Slos et al. | 2 isolates from Peru | JU2585 | SEQUENCED Blaxter | Caenorhabditis DB | BIORXIV | - | |
sulstoni | 32 | SB454 | F/M | - | East Africa? | Feb 2013 | W. Sudhaus | Japonica group, sister of afra | Japonica | 1 isolate, from the gut of the millipede Archispirostreptus gigas | JU2788 | SEQUENCED Blaxter | Caenorhabditis DB | BIORXIV | - |
sp. 33 | 33 | BRC20065 | F/M | J. Wang | Taiwan | 24 May 2012 | J. Wang | Elegans | Briggsae | 1 isolate from Taiwan | BRC20066 | IN SEQUENCING Wang Tsai | - | - | - |
inopinata | 34 | NK74SC | F/M | N. Kanzaki | Shigaki Island, Japan | May 2013 | N. Kanzaki | Elegans | Elegans supergroup, with C. sp. 35 sister of C. elegans | 1 isolate from Japan. Associated with fig wasps and Ficus septica | - | SEQUENCED Kanzaki, Kikuchi | Caenorhabditis DB | - | - |
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 | - | IN SEQUENCING Kanzaki, Kikuchi | - | - | - | |
sp. 36 | 36 | NK02NV | F/M | N. Kanzaki | Tokyo, Japan | Apr 2013 | N. Kanzaki | Japonica group | Japonica | 1 isolate from Japan. Associated with the weevil Niphades variegatus | - | IN SEQUENCING Kanzaki, Kikuchi | - | - | - |
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 | Angaria | 1 isolate from French Guiana | - | IN SEQUENCING Blaxter | - | - | - |
quiockensis | 38 | JU2745 | F/M | F. Besnard | Guadeloupe (Basse Terre) | 09 June 2014 | F. Besnard | Angaria group | Angaria | 1 isolate from Guadeloupe | JU2809 | SEQUENCED Blaxter | Caenorhabditis DB | BIORXIV | - |
waitukubuli | 39 | NIC564 | F/M | C. Braendle | Dominica | 13 May 2014 | C. Braendle | Japonica group | Japonica | 1 isolate from Dominique | - | SEQUENCED Blaxter | Caenorhabditis DB | BIORXIV | - |
tribulationis | 40 | JU2774 | F/M | J.-B. Pénigault | Danbulla, Australia | 08 August 2014 | L. Frézal | Briggsae subgroup, close relative of C. sinica | Briggsae | 5 isolates from Australia, in fresh or rotting figs | JU2818 | SEQUENCED Blaxter | Caenorhabditis DB | BIORXIV | - |
sp. 41 | 41 | BRC20276 | F/M | - | Solomon Islands | October 2014 | J. Wang | Briggsae subgroup, sister species of C. sp. 40 | Briggsae | 2 isolates from Solomon Islands | - | IN SEQUENCING Wang Tsai | - | - | - |
sp. 42 | 42 | NIC1040 | F/M | C. Braendle/A. Cutter | Nouragues Forest, French Guiana | August 2014 | C. Braendle | Drosophilae super group | Drosophilae | one isolate from French Guiana | - | IN SEQUENCING Blaxter | - | - | - |
vivipara | 43 | NIC1070 | F/M | C. Gosse | Chichén Itzá, Yucatán, Mexico | 17 October 2014 | C. Braendle | Drosophilae super group | Drsophilae | 2 isolates from Mexico; in orange berries | NIC1581 | SEQUENCED_draft Blaxter | Caenorhabditis DB | BIORXIV | resequencing required |
sp. 44 | 44 | BRC20300 | F/M | J. Wang | Shihting mountain near Taipei City, Taiwan | Dec 2014 | J. Wang | sister species of C. brenneri | one isolate from Taiwan; in flowers | - | IN SEQUENCING Wang Tsai | - | - | - | |
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 | - | IN SEQUENCING Blaxter | - | - | - | |
sp. 46 | 46 | NIC1120 | F/M | C. Braendle | Macchu Picchu, Aguas Calientes, Peru | 7 April 2015 | C. Braendle | Japonica group | Japonica | one isolate from Peru | - | Sequencing_planned Blaxter | - | - | - |
sp. 47 | 47 | NIC1127 | F/M | C. Braendle | Tambopata region, Amazon, Peru | 7 April 2015 | C. Braendle | Angaria group | Angaria | one isolate from Peru | - | Sequencing_planned Blaxter | - | - | - |
sp. 48 | 48 | BRC20359 | F/M | J. Wang | Khao Yai National park, Thailand | 4 May 2015 | J. Wang | sister of C. brenneri | Brenneri | one isolate from Thailand | - | Sequencing_planned Blaxter | - | - | - |
sp. 49 | 49 | BRC20376 | F/M | J. Wang | Solomon Islands | - | J. Wang | Japonica group? | Japonica | one isolate Solomon Islands | - | Sequencing_planned Blaxter | - | - | - |
sp. 50 | 50 | BRC20387 | F/M | Dai | near Taipei City, Taiwan | 18 October 2015 | J. Wang | Elegans | Elegans | two isolates from Taiwan | - | Sequencing_planned Blaxter | - | - | - |
sp. 51 | 51 | QG2915 | F/M | M. Rockman | Australia | 2017 | M Rockman | Elegans | Elegans | one isolate from Australia | - | Sequencing_planned Blaxter | - | - | - |
sp. 52 | 52 | QG2933 | F/M | M. Rockman | Australia | 2017 | M Rockman | Drosophilae | one isolate from Australia | - | Sequencing_planned Blaxter | - | - | - | |
sp. 53 | 53 | ECA821 | F/M | E. Andersen | Oahu, Hawaii | 2017 | T Crombie | sister of C. kamaaina | several isolates from Oahu and Kauai | - | Sequencing_planned Blaxter | - | - | - | |
sp. 54 | 54 | BRC20468 | F/M | Hsueh, Yen-Ping | Miaoli County?, Taiwan | 18 August 2016 | J Wang | Elegans | - | Sequencing_planned Blaxter | - | - | - | ||
sp. 55 | 55 | JU3317 | F/M | M.-A. Félix | Pugao Laozhai, Yuanyang, Yunnan, China | 5 March 2018 | M.-A. Félix | Elegans | one isolate from Yunnan, China | - | Sequencing_planned Blaxter | - | - | - | |
sp. 56 | 56 | JU2215 | F/M | M. Joron | Tarapoto, Peru | October 2012 | L. Frézal | Angaria group, close to spp. 8 and 24 | Angaria | one isolate from Peru | (JU3313 8x inbred and very sick) | Sequencing_planned Blaxter | - | - | - |
sp. 57 | 57 | QG3050 | F/M | M. Rockman | Barro Colorado Island, Panama | August 2018 | M. Rockman | near monodelphis and sonorae? | two isolates from Panama | in inbreeding | - | - | - |
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
2017 phylogeny of a subset of species, based on their genome sequences by Slos et al.
https://bmczool.biomedcentral.com/articles/10.1186/s40850-017-0013-2
See also BIORXIV