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''
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{| class="wikitable"
 
{| class="wikitable"
  
'''
 
01 Sep 2016 The Blaxter lab website has moved to http://caenorhabditis.org/
 
'''
 
01 July 2015: The Blaxter lab, with support from [http://genomics.ed.ac.uk Edinburgh Genomics], has sequenced 18 further species and launched the ''Caenorhabditis Genomes Project'', see http://caenorhabditis.bio.ed.ac.uk/'''
 
There is a BLAST server for the new genome data in [http://bang.bio.ed.ac.uk:4567/ Edinburgh] and the new raw and preliminary assemblies can be downloaded from [ftp://bang.bio.ed.ac.uk/caenorhabditis/ the Blaxter lab FTP site].
 
 
 
 
|-
 
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! 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://caenorhabditis.org/
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! 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
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|-
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| elegans || a || N2 || H/M || - || - || - || - || Elegans || 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 || 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 || 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 || SEQUENCED 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] || -
 +
|-
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| sp. 2 || 2 || DF5070 || F/M || S. Wirth || Corsica, France || Oct 2001 || W. Sudhaus || Drosophilae || (sister of drosophilae) || 1 single isolate || - || SEQUENCED Blaxter || - || - || -
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|-
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| angaria || 3 || PS1010 || F/M || - || - || 1990 || - || 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
 +
|-
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| sinica || 5 ||  || F/M || M.-A. Félix || Chengyang, Guangxi, China || 6 May 2005 || M.-A. Félix || Elegans || Elegans || Isolates from China, Vietnam (Cutter, Ailion, Félix) || JU800 || SEQUENCED Cutter Blaxter || [http://wormbase.org WORMBASE] || - || -
 
|-
 
|-
| '''''angaria''''' || 3 || PS1010 || F/M ||  || ||1990 || || ''Drosophilae'' super-group, ''Angaria'' group || 3 isolates from Florida USA || - || Mortazavi et al. 2010 Genome Research, '''@Wormbase'''
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| portoensis || 6 || EG4788 || F/M || M. Ailion, A.-J. Rodrigues || Amares, Portugal || 28 Mar 2007 || M. Ailion || || || Portugal, Spain, France, Ireland (Ailion, Félix, Braendle) || EG5626 || Sequenced Blaxter || - || - || -
 
|-
 
|-
| '''''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
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| afra || 7 || JU1199 || F/M || M. Herrmann || Begoro, Ghana || Jun 2007 || M.-A. Félix || Elegans || Japonica || 2 isolates from West Africa (Félix) || JU1286 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || -
 
|-
 
|-
| '''''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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| sp. 8 || 8 || QX1182 || F/M || M. Rockman || Backyard of 93 Mercer St., Jersey City, NJ, USA || 28 Jul 2007 || M. Rockman || Angaria || close to sp. 24 and 56|| Isolates from USA (Fitch), Europe (Braendle, Félix), Canada (Rockman) || JU3312 || SEQUENCED Blaxter || - || - || -
 
|-
 
|-
| '''''drosophilae''''' || # || DF5077 ||F/M || || || || || ''Drosophilae'' group || rotting saguaro cactus in Arizona, a few isolates || DF5112 ||  
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| nigoni || 9 || JU1325 || F/M || M.-A. Félix || Trivandrum Zoo, Kerala, India || 21 Dec 2007 || M.-A. Félix || Elegans || Elegans, sister of 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] || - || -  
|-'''
 
| '''''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'''
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| doughertyi || 10 || JU1333 || F/M || M.-A. Félix || Angela Spice Garden, Kerala, India || 27 Dec 2007 || M.-A. Félix || Elegans || Elegans|| 6 isolates from South India || JU1771 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || RNA seq for JU1328 & JU1333
 
|-
 
|-
| '''''plicata''''' || # || SB355 || F/M || || || || || || || || Blaxter, preliminary assembly available. High proportion of bacterial DNA. Has been reprepared in Felix lab.
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| tropicalis || 11 || JU1373 || H/M || V. Robert, L. Sablé || Saint-Benoît, La Réunion || Jan 2008 || M.-A. Félix || Elegans || Elegans|| Common in tropical regions (not so far on the African continent, one in Asia) || - || SEQUENCED WashU, etc || [http://wormbase.org WORMBASE] || - || -
 
|-
 
|-
| '''''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
+
| castelli || 12 || JU1426 || F/M || P. Châtelet || Nouragues Forest, French Guiana || May 2008 || M.-A. Félix || Angaria || || Several isolates from French Guiana (Félix, Braendle, Cutter) || JU1956 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || -
 
|-
 
|-
| '''''monodelphis ''''' || 1 || SB341 || F/M || J. Raschka  || Berlin, Germany  || 2001  || W. Sudhaus || base of ''Caenorhabditis'' || A second isolate from Norway (Félix) || JU1667  || Blaxter assembly v1  '''http://ensembl.caenorhabditis.org/Caenorhabditis_sp1_v1/Info/Index''' Slos et al. BMC Zool. 2017 ||  
+
| virilis  || 13 || JU1528 || F/M || M.-A. Félix || Orsay apple orchard || 9 Sep 2008 || M.-A. Félix || Drosophilae || || Several isolates from two locations in France || JU1968 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || -
 
|-
 
|-
| '''sp. 2''' || 2 || DF5070 || F/M || S. Wirth  || Corsica, France || Oct 2001 || W. Sudhaus || ''Drosophilae'' group, sister of ''C. drosophilae''  || 1 single isolate || ||  
+
| imperialis || 14 || EG5716 || F/M || D. Ailion || Moorea, French Polynesia || 24 Jul 2009 || M. Ailion || Elegans || Japonica || also Polynesia, Guadeloupe (Félix, Braendle) || EG5942-EG5947 || SEQUENCED Blaxter || - || - || -
 
|-
 
|-
| '''''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'''
+
| kamaaina || 15 || QG122 || F/M || M. Rockman || Near Hanalei Bay, Kauai, Hawaii, USA || 2 Aug 2009 || M. Rockman || Elegans || Elegans || Kauai and Maui, 2 isolates || QG2076, QG2077 || SEQUENCED Rockman || [http://caenorhabditis.org Caenorhabditis DB] || - || 
 
|-
 
|-
| '''''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 ||  sent to Blaxter
+
| wallacei  || 16 || JU1873 || F/M || J.-B. Pénigault || Sanda Center, Bali, Indonesia || 11 Nov 2009 || J.-B. Pénigault || Elegans || Elegans || 2 isolates from Indonesia (Félix) || JU1898 || in assembly Schwarz || || - ||   
 
|-
 
|-
| '''''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. Resequenced by Blaxter, assembly v1 '''http://ensembl.caenorhabditis.org/Caenorhabditis_afra_v1/Info/Index'''
+
| nouraguensis  || 17 || JU1825 || F/M || C. Braendle, M.-A. Félix || Nouragues Forest, French Guiana || 21 Nov 2009 || C. Braendle, M.-A. Félix || Elegans || Japonica || Many isolates from French Guiana || JU2079 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || additional strains sequenced
 
|-
 
|-
| '''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)  ||  
+
| macrosperma  || 18 || JU1857 || F/M || C. Braendle, M.-A. Félix || Nouragues Forest, French Guiana || 23 Nov 2009 || C. Braendle, M.-A. Félix || Elegans || Japonica || A few isolates from Nouragues, French Guiana || JU2083 || SEQUENCED Cutter || [http://caenorhabditis.org Caenorhabditis DB] || - || -
 
|-
 
|-
|'''''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
+
| yunquensis  || 19 || EG6142 || F/M || S. Dalton || El Yunque, Puerto Rico || 28 Mar 2010 || S. Dalton, M. Ailion || Elegans || Japonica || Puerto Rico || XZ1517-XZ1520 || SEQUENCED Blaxter || - || - || -
 
|-
 
|-
|'''''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 https://www.ncbi.nlm.nih.gov/bioproject/PRJEB11002, preliminary assembly available;  RNA seq for JU1328 & JU1333
+
| guadeloupensis  || 20 || NIC113 || F/M || C. Braendle || Soufrière Forest trail, Guadeloupe || Mar 2010 || C. Braendle || Guadeloupensis ||  || Guadeloupe ||  || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || - || resequencing required
 
|-
 
|-
| '''''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'''
+
| 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://onlinelibrary.wiley.com/doi/10.1002/evl3.110 Stevens et al. Evol Lett 2019] || -
 
|-
 
|-
| '''''castelli''''' || 12 || JU1426 || F/M || P. Châtelet || Nouragues Forest, French Guiana || May 2008 || M.-A. Félix || ''Angaria'' group || Several isolates from French Guiana (Félix, Braendle, Cutter) || JU1956  || Blaxter, sequenced https://www.ncbi.nlm.nih.gov/bioproject/PRJEB11356
+
| latens || 23 || VX88 || F/M || G.-X. Wang || Jiufeng Village, Wuhan City, Hubei Province, China || 27 Oct 2009 || G.-X. Wang || Elegans || Elegans, sister of C. remanei || Several isolates from China (Cutter) || PX534, PX573, PX574, PX580 || SEQUENCED Phillips || [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 || Blaxter assembly v1 '''http://ensembl.caenorhabditis.org/Caenorhabditis_virilis_v1/Info/Index'''
+
| sp. 24 || 24 || QG555 || F/M || A. Paaby || Santa Barbara, USA || July 2011 || A. Paaby || Angaria || close to sp. 8 and 56|| Isolates from California, Panama, Mexico (Rockman, Félix) || || SEQUENCED Blaxter || - || - || -
 
|-
 
|-
| '''''imperialis''''' || 14 || EG5716 || F/M || D. Ailion || Moorea, French Polynesia  || 24 Jul 2009  || M. Ailion || ''Japonica'' group || also Polynesia, Guadeloupe (Félix, Braendle)  || EG5942-EG5947 || sent to Blaxter
+
| sp. 25 || 25 || ZF1222 || F/M || A. Seah, T. Inoue || Singapore || 3 Sep 2011 || T. Inoue || Elegans || Japonica || 2 isolates from Singapore || ZF1457 || SEQUENCED 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 || under assembly, Rockman
+
| zanzibari || 26 || JU2161 || F/M || M.-A. Félix || Zanzibar, Tanzania || 9 Mar 2012 || M.-A. Félix || Elegans || Elegans || 5 isolates from Zanzibar || JU2190 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://onlinelibrary.wiley.com/doi/10.1002/evl3.110 Stevens et al. Evol Lett 2019] || -
 
|-
 
|-
| '''''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 || Blaxter preliminary assembly available, Erich Schwarz PacBio
+
| sp. 27 || 27 || QX2263 || F/M || - || Buenos Aires, Argentina || 2 Mar 2012 || E. Andersen || || Portoensis || Argentina ||  || SEQUENCED Blaxter || - || - || -
 
|-
 
|-
| '''''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 https://www.ncbi.nlm.nih.gov/bioproject/PRJEB10884, preliminary assembly available ; additional strains sequenced also
+
| panamensis || 28 || QG702 || F/M || M. Rockman || Barro Colorado Island, Panama || 23 Apr 2012 || M. Rockman || Elegans|| Japonica || several isofemale lines from Panama || QG2080, QG2081 || SEQUENCED Rockman || [http://caenorhabditis.org Caenorhabditis DB] || [https://onlinelibrary.wiley.com/doi/10.1002/evl3.110 Stevens et al. Evol Lett 2019] || -
 
|-
 
|-
| '''''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  || Blaxter https://www.ncbi.nlm.nih.gov/bioproject/PRJEB10887, preliminary assembly available
+
| becei || 29 || QG704 || F/M || M. Rockman || Barro Colorado Island, Panama || 25 Apr 2012 || M. Rockman || Elegans || Japonica, sister of nouraguensis || many isofemale lines from Panama || QG2082, QG2083 || SEQUENCED Rockman || [http://caenorhabditis.org Caenorhabditis DB] || [https://onlinelibrary.wiley.com/doi/10.1002/evl3.110 Stevens et al. Evol Lett 2019] || -
 
|-
 
|-
| '''''yunquensis ''''' || 19 || EG6142 ||F/M || S. Dalton  || El Yunque, Puerto Rico || 28 Mar 2010 || S. Dalton, M. Ailion || ''Japonica'' group  || Puerto Rico || XZ1517-XZ1520 || sent to Blaxter
+
| sp. 30 || 30 || DF5152 || F/M || - || Gallon Jug, Belize || 15 Nov 2012 || K. Kiontke || Drosophilae ||  || 4 isofemale lines from Belize || ongoing (K. Kiontke) || SEQUENCED Blaxter || - || - || -
 
|-
 
|-
| '''''guadeloupensis ''''' || 20 || NIC113 || F/M || C. Braendle || Soufrière Forest trail, Guadeloupe || Mar 2010  || C. Braendle || ''Drosophilae'' supergroup || Guadeloupe || ||   Blaxter https://www.ncbi.nlm.nih.gov/bioproject/PRJEB11393, preliminary assembly available
+
| uteleia || 31 || JU2469 || F/M || - || Madre de Dios, Peru || Jan 2013 || L. Frézal || Guadeloupensis ||| 2 isolates from Peru || JU2585 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://onlinelibrary.wiley.com/doi/10.1002/evl3.110 Stevens et al. Evol Lett 2019] || -
 
|-
 
|-
| '''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 https://www.ncbi.nlm.nih.gov/bioproject/PRJEB12595/, preliminary assembly available
+
| sulstoni || 32 || SB454 || F/M || - || East Africa? || Feb 2013 || W. Sudhaus || Elegans || Japonica, sister of afra || 1 isolate, from the gut of the millipede Archispirostreptus gigas || JU2788 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://onlinelibrary.wiley.com/doi/10.1002/evl3.110 Stevens et al. Evol Lett 2019] || -
 
|-
 
|-
| '''''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. 33 || 33 || BRC20065 || F/M || J. Wang || Taiwan || 24 May 2012 || J. Wang || Elegans || Elegans || 1 isolate from Taiwan || BRC20066 || IN SEQUENCING Wang Tsai || - || - || -
 
|-
 
|-
| '''sp. 24''' || 24 || QG555 || F/M || A. Paaby  || Santa Barbara, USA || July 2011 || A. Paaby || ''Angaria'' group, sister of sp. || Isolates from California, Panama, Mexico (Rockman, Félix)  ||   ||
+
| inopinata || 34 || NK74SC || F/M || N. Kanzaki || Shigaki Island, Japan || May 2013 || N. Kanzaki || Elegans || Elegans, 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] || [https://www.nature.com/articles/s41467-018-05712-5 Kanzaki et al. Nat Comm 2019] || -
 
|-
 
|-
| '''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. 35 || 35 || DF5171 || F/M || - || Banda Ache, Indonesia || Aug 2013 || N. Kanzaki || Elegans || Elegans, with C. sp. 34 sister of C. elegans || 2 Isolates from Indonesia, associated with Ficus hispida || - || IN SEQUENCING Kanzaki, Kikuchi || - || - || -
 
|-
 
|-
| '''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 https://www.ncbi.nlm.nih.gov/bioproject/PRJEB12596/, preliminary assembly available
+
| sp. 36 || 36 || NK02NV || F/M || N. Kanzaki || Tokyo, Japan || Apr 2013 || N. Kanzaki || Elegans || Japonica || 1 isolate from Japan. Associated with the weevil Niphades variegatus || - || IN SEQUENCING Kanzaki, Kikuchi || - || - || -
 
|-
 
|-
| '''sp. 27''' || 27 || QX2263 || F/M || || Buenos Aires, Argentina  || 2 Mar 2012  || E. Andersen  || ''Drosophilae'' supergroup, sister of ''portoensis''  || Argentina ||   ||
+
| dolens || 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 || - || SEQUENCED Blaxter || - || - || -
 
|-
 
|-
| '''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
+
| quiockensis || 38 || JU2745 || F/M || F. Besnard || Guadeloupe (Basse Terre) || 09 June 2014 || F. Besnard || Angaria|| || 1 isolate from Guadeloupe || JU2809 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://onlinelibrary.wiley.com/doi/10.1002/evl3.110 Stevens et al. Evol Lett 2019] || -
 
|-
 
|-
| '''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 || under assembly, Rockman
+
| waitukubuli || 39 || NIC564 || F/M || C. Braendle || Dominica || 13 May 2014 || C. Braendle || Elegans || Japonica || 1 isolate from Dominique || - || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://onlinelibrary.wiley.com/doi/10.1002/evl3.110 Stevens et al. Evol Lett 2019] || -
 
|-
 
|-
| '''sp. 30''' || 30 || DF5152  || F/M ||   || Gallon Jug, Belize  || 15 Nov 2012 || K. Kiontke  || ''Drosophilae'' subgroup  || 4 isofemale lines from Belize  || ongoing (K. Kiontke)  ||
+
| tribulationis || 40 || JU2774 || F/M || J.-B. Pénigault || Danbulla, Australia || 08 August 2014 || L. Frézal || Elegans|| Elegans || 5 isolates from Australia, in fresh or rotting figs || JU2818 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://onlinelibrary.wiley.com/doi/10.1002/evl3.110 Stevens et al. Evol Lett 2019] || -
 
|-
 
|-
|| '''sp. 31''' || 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 || Blaxter https://www.ncbi.nlm.nih.gov/bioproject/PRJEB12600/, preliminary assembly available  ||
+
| sp. 41 || 41 || BRC20276 || F/M || - || Solomon Islands || October 2014 || J. Wang || Elegans || Elegans || 2 isolates from Solomon Islands || - || IN SEQUENCING Wang Tsai || - || - || -
 
|-
 
|-
| '''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 assembly v1 '''http://ensembl.caenorhabditis.org/Caenorhabditis_sp32_v1/Info/Index'''
+
| astrocarya || 42 || NIC1040 || F/M || C. Braendle/A. Cutter || Nouragues Forest, French Guiana || August 2014 || C. Braendle || base || || one isolate from French Guiana || - || SEQUENCED Blaxter || - || - || -
 
|-
 
|-
| '''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
+
| vivipara || 43 || NIC1070 || F/M || C. Gosse || Chichén Itzá, Yucatán, Mexico || 17 October 2014 || C. Braendle ||  || Portoensis || 2 isolates from Mexico; in orange berries || NIC1581 || SEQUENCED Blaxter || [http://caenorhabditis.org Caenorhabditis DB] || [https://onlinelibrary.wiley.com/doi/10.1002/evl3.110 Stevens et al. Evol Lett 2019] || resequencing required
 
|-
 
|-
| '''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. 44 || 44 || BRC20300 || F/M || J. Wang || Shihting mountain near Taipei City, Taiwan || Dec 2014 || J. Wang || Elegans || Elegans || one isolate from Taiwan; in flowers || - || IN SEQUENCING Wang Tsai || - || - || -
 
|-
 
|-
| '''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. 45 || 45 || NIC759 || F/M || C. Braendle || Sylvania, Dominica || 16 May 2014 || C. Braendle || Guadeloupensis || sister species of C. guadeloupensis || one isolate from Dominica; in Cecropia fruit || - || SEQUENCED Blaxter || - || - || -
 
|-
 
|-
| '''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. 46 || 46 || NIC1120 || F/M || C. Braendle || Macchu Picchu, Aguas Calientes, Peru || 7 April 2015 || C. Braendle || Elegans|| Japonica || one isolate from Peru || - || SEQUENCED Blaxter|| - || - || -
 
|-
 
|-
| '''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. 47 || 47 || NIC1127 || F/M || C. Braendle || Tambopata region, Amazon, Peru || 7 April 2015 || C. Braendle || Angaria || || one isolate from Peru || - || SEQUENCED Blaxter || - || - || -
 
|-
 
|-
| '''sp. 38''' || 38 || JU2745  || F/M || F. Besnard  || Guadeloupe (Basse Terre) || 09 June 2014 || F. Besnard  || ''Angaria'' group  || 1 isolate from Guadeloupe  || JU2809 || Blaxter assembly v1 '''http://ensembl.caenorhabditis.org/Caenorhabditis_sp38_v1/Info/Index'''
+
| sp. 48 || 48 || BRC20359 || F/M || J. Wang || Khao Yai National park, Thailand || 4 May 2015 || J. Wang || Elegans || Elegans || one isolate from Thailand || - || SSEQUENCED Blaxter || - || - || -
 
|-
 
|-
| '''sp. 39''' || 39 || NIC564  || F/M || C. Braendle || Dominica || 13 May 2014 || C. Braendle  || ''Japonica'' group  || 1 isolate from Dominique  ||   || Blaxter, sequenced https://www.ncbi.nlm.nih.gov/bioproject/PRJEB12602/
+
| sp. 49 || 49 || BRC20376 || F/M || J. Wang || Solomon Islands || - || J. Wang || Elegans || Japonica || one isolate Solomon Islands || - || SEQUENCED Blaxter || - || - || -
 
|-
 
|-
| '''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 assembly v1 '''http://ensembl.caenorhabditis.org/Caenorhabditis_sp40_v1/Info/Index'''
+
| sp. 50 || 50 || BRC20387 || F/M || Dai || near Taipei City, Taiwan || 18 October 2015 ||J. Wang || Elegans || Japonica || two isolates from Taiwan || - || Sequencing_planned Blaxter || - || - || -
 
|-
 
|-
| '''sp. 41''' || 41 || BRC20276 || F/M || || Solomon Islands || October 2014  || J. Wang || ''Briggsae'' subgroup, sister species of C. sp. 40  || 2 isolates from Solomon Islands || ||
+
| sp. 51 || 51 || QG2915 || F/M || M. Rockman || Australia || 2017 || M Rockman || Elegans || Elegans || two isolates from Australia || - || SEQUENCED Blaxter || - || - || -
 
|-
 
|-
| '''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. 52 || 52 || QG2933 || F/M || M. Rockman || Australia || 2017 || M Rockman || ||  || one isolate from Australia || - || Sequencing_planned Blaxter || - || - || -
 
|-
 
|-
| '''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 || ||  
+
| sp. 53 || 53 || ECA821 || F/M || E. Andersen || Oahu, Hawaii || 2017 || T Crombie || Elegans || Elegans, sister of C. kamaaina || several isolates from Oahu and Kauai || - || SEQUENCED Blaxter || - || - || -
 
|-
 
|-
| '''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. 54 || 54 || BRC20468 || F/M || Hsueh, Yen-Ping || Miaoli County?, Taiwan || 18 August 2016 || J Wang || Elegans || Elegans || || - || SEQUENCED Blaxter|| - || - || -
 
|-
 
|-
| '''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. 55 || 55 || JU3317 || F/M || M.-A. Félix || Pugao Laozhai, Yuanyang, Yunnan, China || 5 March 2018 || M.-A. Félix || Elegans || Elegans || one isolate from Yunnan, China || - ||SEQUENCED Blaxter || - || - || -
 
|-
 
|-
| '''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. 56 || 56 || JU2215 || F/M || M. Joron || Tarapoto, Peru || October 2012 || L. Frézal || Angaria || close to sp. 8 and 24|| one isolate from Peru || (JU3313 8x inbred and very sick) || SEQUENCED 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 || QG3077 ||  || - || - || -
 
|-
 
|-
| '''sp. 47''' || 47 || NIC1127 || F/M || C. Braendle  || Tambopata region, Amazon, Peru ||  7 April 2015  ||C. Braendle || ''Angaria'' group || one isolate from Peru || ||  
+
| sp. 58 || 58 || RS6130 || F/M || M. Herrmann || Bolivia || 2019 ||  M. Herrmann || || close to C. astrocarya  || || JU3779 or JU3880 || sent to Blaxter || - || - || -
 
|-
 
|-
| '''sp. 48''' || 48 || BRC20359 || F/M || J. Wang || Khao Yai National park, Thailand || 4 May 2015  ||J. Wang || sister of ''C. brenneri'' || one isolate from Thailand ||  ||  
+
| sp. 59 || 59 || RS6131 || F/M || M. Herrmann || Bolivia || 2019 ||  M. Herrmann || Elegans || Japonica, close to C. becei || || JU3778 || sent to Blaxter || - || - || -
 +
|-
 +
| sp. 60 || 60 || QG3550 || F/M || M. Rockman || Costa Rica || 2019 ||  M. Rockman || Elegans || Japonica  || one isolate || in inbreeding ||  || - || - || -
 
|-
 
|-
| '''sp. 49''' || 49 || BRC20376 || F/M || J. Wang?  || Solomon Islands ||  ||J. Wang? || ''Japonica'' group? || one isolate Solomon Islands ||  ||  
+
| sp. 61 || 61 || JU4045 || F/M || M.-A. Félix || Sapa area, Vietnam || 2019 ||  M.-A. Félix || Elegans  || Elegans || one isolate || in inbreeding (Felix) ||  || - || - || -
 
|-
 
|-
| '''sp. 50''' || 50 || BRC20387 || F/M || Dai  || near Taipei City, Taiwan ||  18 October 2015 ||J. Wang || ''Elegans'' supergroup || two isolates from Taiwan ||  ||  
+
| sp. 62 || 62 || JU4050 || F/M || M.-A. Félix || Sapa area, Vietnam || 2019 ||  M.-A. Félix || Elegans || Elegans || one isolate || in inbreeding (Felix) ||  || - || - || -
 
|-
 
|-
| '''sp. 51''' || 51 || QG2915 || F/M || M. Rockman  || Australia || 2017 ||M. Rockman || ''Elegans'' supergroup || one isolate from Australia ||  ||  
+
| sp. 63 || 63 || JU4056 || F/M || M.-A. Félix || Sapa area, Vietnam || 2019 || M.-A. Félix || Elegans || Elegans, close to sp. 33 || one isolate || in inbreeding (Felix) ||  || - || - || -
 
|-
 
|-
| '''sp. 52''' || 52 || QG2933 || F/M || M. Rockman  || Australia || 2017 ||M. Rockman || ''Drosophilae'' supergroup || one isolate from Australia ||  ||  
+
| sp. 64 || 64 || JU4061 || F/M || M.-A. Félix || Sapa area, Vietnam || 2019 || M.-A. Félix || || Portoensis  || one isolate || in inbreeding (Felix) ||  || - || - || -
 
|-
 
|-
| '''sp. 53''' || 53 || ECA821 || F/M || E. Andersen  || Oahu, Hawaii ||  2017 ||T. Crombie || sister of ''C. kamaaina'' ||several isolates from Oahu and Kauai  || ||  
+
| sp. 65 || 65 || JU4086 || F/M || M.-A. Félix || Dalat area, Vietnam || 2019 ||  M.-A. Félix || Elegans  || Elegans || four isolates from Vietnam || in inbreeding (Felix) ||  || - || - || -
 
|-
 
|-
| '''sp. 54''' || 54 || BRC20468|| F/M || Hsueh, Yen-Ping  || Miaoli County?, Taiwan || 18 August 2016 ||J. Wang || ''Elegans'' group ||one isolate from Taiwan ||  ||  
+
| sp. 66 || 66 || JU4096 || F/M || M.-A. Félix || Dalat area, Vietnam || 2019 || M.-A. Félix || Elegans  || Elegans, close to sp. 48 and brenneri || seven isolates from Vietnam || in inbreeding (Felix) ||  || - || - || -
 
|-
 
|-
| '''sp. 55''' || 55 || JU3317|| F/M || M.-A. Félix  || Pugao Laozhai, Yuanyang, Yunnan, China || 5 March 2018  || M.-A. Félix || ''Elegans'' group?  ||one isolate from Yunnan, China ||  ||
 
 
|}
 
|}
  
Line 151: Line 169:
  
 
https://bmczool.biomedcentral.com/articles/10.1186/s40850-017-0013-2
 
https://bmczool.biomedcentral.com/articles/10.1186/s40850-017-0013-2
 +
 +
'''See Stevens et al. 2019'''
 +
[https://onlinelibrary.wiley.com/doi/10.1002/evl3.110]
 +
 +
'''and the latest unpublished phylogeny'''
 +
[http://caenorhabditis.org/?page_id=151]. Thank you Lewis!

Revision as of 17:33, 21 January 2020

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 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 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 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 SEQUENCED 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 - SEQUENCED Blaxter - - -
angaria 3 PS1010 F/M - - 1990 - 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 Elegans 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 Portugal, Spain, France, Ireland (Ailion, Félix, Braendle) EG5626 Sequenced Blaxter - - -
afra 7 JU1199 F/M M. Herrmann Begoro, Ghana Jun 2007 M.-A. Félix Elegans 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 close to sp. 24 and 56 Isolates from USA (Fitch), Europe (Braendle, Félix), Canada (Rockman) JU3312 SEQUENCED Blaxter - - -
nigoni 9 JU1325 F/M M.-A. Félix Trivandrum Zoo, Kerala, India 21 Dec 2007 M.-A. Félix Elegans Elegans, sister of 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 Elegans Elegans 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 Elegans Elegans Common in tropical regions (not so far on the African continent, one in Asia) - SEQUENCED WashU, etc WORMBASE - -
castelli 12 JU1426 F/M P. Châtelet Nouragues Forest, French Guiana May 2008 M.-A. Félix 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 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 Elegans Japonica also Polynesia, Guadeloupe (Félix, Braendle) EG5942-EG5947 SEQUENCED Blaxter - - -
kamaaina 15 QG122 F/M M. Rockman Near Hanalei Bay, Kauai, Hawaii, USA 2 Aug 2009 M. Rockman Elegans Elegans 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 Elegans Elegans 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 Elegans Japonica 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 Elegans Japonica 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 Elegans Japonica Puerto Rico XZ1517-XZ1520 SEQUENCED Blaxter - - -
guadeloupensis 20 NIC113 F/M C. Braendle Soufrière Forest trail, Guadeloupe Mar 2010 C. Braendle Guadeloupensis Guadeloupe SEQUENCED 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 Stevens et al. Evol Lett 2019 -
latens 23 VX88 F/M G.-X. Wang Jiufeng Village, Wuhan City, Hubei Province, China 27 Oct 2009 G.-X. Wang Elegans Elegans, 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 close to sp. 8 and 56 Isolates from California, Panama, Mexico (Rockman, Félix) SEQUENCED Blaxter - - -
sp. 25 25 ZF1222 F/M A. Seah, T. Inoue Singapore 3 Sep 2011 T. Inoue Elegans Japonica 2 isolates from Singapore ZF1457 SEQUENCED Blaxter - - -
zanzibari 26 JU2161 F/M M.-A. Félix Zanzibar, Tanzania 9 Mar 2012 M.-A. Félix Elegans Elegans 5 isolates from Zanzibar JU2190 SEQUENCED Blaxter Caenorhabditis DB Stevens et al. Evol Lett 2019 -
sp. 27 27 QX2263 F/M - Buenos Aires, Argentina 2 Mar 2012 E. Andersen Portoensis Argentina SEQUENCED Blaxter - - -
panamensis 28 QG702 F/M M. Rockman Barro Colorado Island, Panama 23 Apr 2012 M. Rockman Elegans Japonica several isofemale lines from Panama QG2080, QG2081 SEQUENCED Rockman Caenorhabditis DB Stevens et al. Evol Lett 2019 -
becei 29 QG704 F/M M. Rockman Barro Colorado Island, Panama 25 Apr 2012 M. Rockman Elegans Japonica, sister of nouraguensis many isofemale lines from Panama QG2082, QG2083 SEQUENCED Rockman Caenorhabditis DB Stevens et al. Evol Lett 2019 -
sp. 30 30 DF5152 F/M - Gallon Jug, Belize 15 Nov 2012 K. Kiontke Drosophilae 4 isofemale lines from Belize ongoing (K. Kiontke) SEQUENCED Blaxter - - -
uteleia 31 JU2469 F/M - Madre de Dios, Peru Jan 2013 L. Frézal Guadeloupensis 2 isolates from Peru JU2585 SEQUENCED Blaxter Caenorhabditis DB Stevens et al. Evol Lett 2019 -
sulstoni 32 SB454 F/M - East Africa? Feb 2013 W. Sudhaus Elegans Japonica, sister of afra 1 isolate, from the gut of the millipede Archispirostreptus gigas JU2788 SEQUENCED Blaxter Caenorhabditis DB Stevens et al. Evol Lett 2019 -
sp. 33 33 BRC20065 F/M J. Wang Taiwan 24 May 2012 J. Wang Elegans Elegans 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, with C. sp. 35 sister of C. elegans 1 isolate from Japan. Associated with fig wasps and Ficus septica - SEQUENCED Kanzaki, Kikuchi Caenorhabditis DB Kanzaki et al. Nat Comm 2019 -
sp. 35 35 DF5171 F/M - Banda Ache, Indonesia Aug 2013 N. Kanzaki Elegans Elegans, 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 Elegans Japonica 1 isolate from Japan. Associated with the weevil Niphades variegatus - IN SEQUENCING Kanzaki, Kikuchi - - -
dolens 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 - SEQUENCED Blaxter - - -
quiockensis 38 JU2745 F/M F. Besnard Guadeloupe (Basse Terre) 09 June 2014 F. Besnard Angaria 1 isolate from Guadeloupe JU2809 SEQUENCED Blaxter Caenorhabditis DB Stevens et al. Evol Lett 2019 -
waitukubuli 39 NIC564 F/M C. Braendle Dominica 13 May 2014 C. Braendle Elegans Japonica 1 isolate from Dominique - SEQUENCED Blaxter Caenorhabditis DB Stevens et al. Evol Lett 2019 -
tribulationis 40 JU2774 F/M J.-B. Pénigault Danbulla, Australia 08 August 2014 L. Frézal Elegans Elegans 5 isolates from Australia, in fresh or rotting figs JU2818 SEQUENCED Blaxter Caenorhabditis DB Stevens et al. Evol Lett 2019 -
sp. 41 41 BRC20276 F/M - Solomon Islands October 2014 J. Wang Elegans Elegans 2 isolates from Solomon Islands - IN SEQUENCING Wang Tsai - - -
astrocarya 42 NIC1040 F/M C. Braendle/A. Cutter Nouragues Forest, French Guiana August 2014 C. Braendle base one isolate from French Guiana - SEQUENCED Blaxter - - -
vivipara 43 NIC1070 F/M C. Gosse Chichén Itzá, Yucatán, Mexico 17 October 2014 C. Braendle Portoensis 2 isolates from Mexico; in orange berries NIC1581 SEQUENCED Blaxter Caenorhabditis DB Stevens et al. Evol Lett 2019 resequencing required
sp. 44 44 BRC20300 F/M J. Wang Shihting mountain near Taipei City, Taiwan Dec 2014 J. Wang Elegans Elegans 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 Guadeloupensis sister species of C. guadeloupensis one isolate from Dominica; in Cecropia fruit - SEQUENCED Blaxter - - -
sp. 46 46 NIC1120 F/M C. Braendle Macchu Picchu, Aguas Calientes, Peru 7 April 2015 C. Braendle Elegans Japonica one isolate from Peru - SEQUENCED Blaxter - - -
sp. 47 47 NIC1127 F/M C. Braendle Tambopata region, Amazon, Peru 7 April 2015 C. Braendle Angaria one isolate from Peru - SEQUENCED Blaxter - - -
sp. 48 48 BRC20359 F/M J. Wang Khao Yai National park, Thailand 4 May 2015 J. Wang Elegans Elegans one isolate from Thailand - SSEQUENCED Blaxter - - -
sp. 49 49 BRC20376 F/M J. Wang Solomon Islands - J. Wang Elegans Japonica one isolate Solomon Islands - SEQUENCED Blaxter - - -
sp. 50 50 BRC20387 F/M Dai near Taipei City, Taiwan 18 October 2015 J. Wang Elegans Japonica two isolates from Taiwan - Sequencing_planned Blaxter - - -
sp. 51 51 QG2915 F/M M. Rockman Australia 2017 M Rockman Elegans Elegans two isolates from Australia - SEQUENCED Blaxter - - -
sp. 52 52 QG2933 F/M M. Rockman Australia 2017 M Rockman one isolate from Australia - Sequencing_planned Blaxter - - -
sp. 53 53 ECA821 F/M E. Andersen Oahu, Hawaii 2017 T Crombie Elegans Elegans, sister of C. kamaaina several isolates from Oahu and Kauai - SEQUENCED Blaxter - - -
sp. 54 54 BRC20468 F/M Hsueh, Yen-Ping Miaoli County?, Taiwan 18 August 2016 J Wang Elegans Elegans - SEQUENCED Blaxter - - -
sp. 55 55 JU3317 F/M M.-A. Félix Pugao Laozhai, Yuanyang, Yunnan, China 5 March 2018 M.-A. Félix Elegans Elegans one isolate from Yunnan, China - SEQUENCED Blaxter - - -
sp. 56 56 JU2215 F/M M. Joron Tarapoto, Peru October 2012 L. Frézal Angaria close to sp. 8 and 24 one isolate from Peru (JU3313 8x inbred and very sick) SEQUENCED 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 QG3077 - - -
sp. 58 58 RS6130 F/M M. Herrmann Bolivia 2019 M. Herrmann close to C. astrocarya JU3779 or JU3880 sent to Blaxter - - -
sp. 59 59 RS6131 F/M M. Herrmann Bolivia 2019 M. Herrmann Elegans Japonica, close to C. becei JU3778 sent to Blaxter - - -
sp. 60 60 QG3550 F/M M. Rockman Costa Rica 2019 M. Rockman Elegans Japonica one isolate in inbreeding - - -
sp. 61 61 JU4045 F/M M.-A. Félix Sapa area, Vietnam 2019 M.-A. Félix Elegans Elegans one isolate in inbreeding (Felix) - - -
sp. 62 62 JU4050 F/M M.-A. Félix Sapa area, Vietnam 2019 M.-A. Félix Elegans Elegans one isolate in inbreeding (Felix) - - -
sp. 63 63 JU4056 F/M M.-A. Félix Sapa area, Vietnam 2019 M.-A. Félix Elegans Elegans, close to sp. 33 one isolate in inbreeding (Felix) - - -
sp. 64 64 JU4061 F/M M.-A. Félix Sapa area, Vietnam 2019 M.-A. Félix Portoensis one isolate in inbreeding (Felix) - - -
sp. 65 65 JU4086 F/M M.-A. Félix Dalat area, Vietnam 2019 M.-A. Félix Elegans Elegans four isolates from Vietnam in inbreeding (Felix) - - -
sp. 66 66 JU4096 F/M M.-A. Félix Dalat area, Vietnam 2019 M.-A. Félix Elegans Elegans, close to sp. 48 and brenneri seven isolates from Vietnam in inbreeding (Felix) - - -


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

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 Stevens et al. 2019 [1]

and the latest unpublished phylogeny [2]. Thank you Lewis!