Difference between revisions of "LIST OF AVAILABLE CAENORHABDITIS SPECIES and the state of their genome projects"
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'''4 Nov 2014: Great news: Mark Blaxter has obtained funding including direct support from [http://genomics.ed.ac.uk Edinburgh Genomics] to sequence 15-20 further species and launched the ''Caenorhabditis Genomes Project'', see http://caenorhabditis.bio.ed.ac.uk/''' | '''4 Nov 2014: Great news: Mark Blaxter has obtained funding including direct support from [http://genomics.ed.ac.uk Edinburgh Genomics] to sequence 15-20 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 | + | 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://nematodes.org/genomes/index_caenorhabditis.html | ! 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 |
Revision as of 15:25, 27 June 2015
4 Nov 2014: Great news: Mark Blaxter has obtained funding including direct support from Edinburgh Genomics to sequence 15-20 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 Edinburgh and the new raw and preliminary assemblies can be downloaded from the Blaxter lab FTP site.
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, preliminary assembly available. 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 | 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 | sent to Blaxter | |
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 available; 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, preliminary assembly available | |
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 | |
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 | Blaxter preliminary assembly available | |
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, preliminary assembly available; additional strains sequenced also | |
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, preliminary assembly available | |
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 | |
guadeloupensis | 20 | NIC113 | F/M | C. Braendle | Soufrière Forest trail, Guadeloupe | Mar 2010 | C. Braendle | Drosophilae supergroup | Guadeloupe | Blaxter, preliminary assembly available | ||
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, preliminary assembly available | |
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, preliminary assembly available | |
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 | 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, preliminary assembly available | ||
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, preliminary assembly available | ||
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, preliminary assembly available | |
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, preliminary assembly available | |
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, preliminary assembly available | ||
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 | 47 | 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