View source for Nematode sequencing summary

This page summarizes the sequencing efforts on nematode genomes. It is a work in progress and is not definitive.<br> 

'''Last update: 13 June 2008'''<br> 

= Genome Sequencing Efforts<br>  =

{| cellspacing="1" cellpadding="1" border="1" width="100%"
|+ '''Nematode Sequencing Status''' 
|- style="background: burlywood none repeat scroll 0% 50%; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;"
| '''Species'''<br> 
| '''Status'''<br> 
| '''Assembly size'''<br> 
| '''Gene count''' '''(method)'''<br> 
| '''Download'''<br> 
| '''Browser'''<br>
|-
| ''C. elegans''<br> 
| finished; Annotated<br> 
| 101 Mb in 6 chromosomes<br> 
| 20,177 (curated)<br> 
| [ftp://ftp.wormbase.org/pub/wormbase/genomes/elegans/ WormBase]<br> 
| 
[http://www.wormbase.org/db/seq/gbrowse/elegans/ WormBase] 

[http://genome.ucsc.edu/cgi-bin/hgTracks?db=ce6 UCSC] 

|-
| ''C. briggsae''<br> 
| 10x draft; Annotated<br> 
| 101 Mb in 6 chromosomes, 7 Mb unassigned<br> 
| 21,558 (Jigsaw)<br> 
| [ftp://ftp.wormbase.org/pub/wormbase/genomes/briggsae/ WormBase]<br> 
| 
[http://www.wormbase.org/db/seq/gbrowse/briggsae/ WormBase] 

[http://genome.ucsc.edu/cgi-bin/hgTracks?db=cb3 UCSC] 

|-
| ''C. brenneri'' 
| 9.5x draft, initial gene calls<br> 
| 191 Mb in 3510 supercontigs<br> 
| 30,557 (Jigsaw)<br> 
| [ftp://ftp.wormbase.org/pub/wormbase/genomes/brenneri/ WormBase]<br> 
| 
[http://www.wormbase.org/db/seq/gbrowse/brenneri/ WormBase] 

[http://genome.ucsc.edu/cgi-bin/hgTracks?db=caePb2 UCSC] 

|-
| ''C. japonica'' 
| 6.3x draft, initial gene calls<br> 
| 152 Mb in 4657 supercontigs<br> 
| 15,191 (MGENE)<br> 
| [ftp://ftp.wormbase.org/pub/wormbase/genomes/japonica/ WormBase]<br> 
| 
[http://www.wormbase.org/db/seq/gbrowse/japonica/ WormBase] 

[http://genome.ucsc.edu/cgi-bin/hgTracks?db=caeJap1 UCSC] 

|-
| ''C. remanei'' 
| 9.2x draft, initial gene calls<br> 
| 145 Mb in 3670 supercontigs<br> 
| 31,641 (Jigsaw)<br> 
| [ftp://ftp.wormbase.org/pub/wormbase/genomes/remanei/ WormBase]<br> 
| 
[http://www.wormbase.org/db/seq/gbrowse/remanei/ WormBase] 

[http://genome.ucsc.edu/cgi-bin/hgTracks?db=caeRem3 UCSC] 

|-
| ''P. pacificus'' 
| 8.9x draft, initial gene calls <br> 
| 169 Mb in 5106 supercontigs<br> 
| 29,201 (SNAP)<br> 
| [http://genome.wustl.edu/pub/organism/Invertebrates/Pristionchus_pacificus/ WashU]<br> 
| 
[http://www.pristionchus.org/cgi-bin/genome.pl www.pristionchus.org] 

[http://genome.ucsc.edu/cgi-bin/hgTracks?db=priPac1 UCSC] 

|-
| ''B. malayi'' 
| 8.9x draft, genes annotated<br> 
| 72 Mb in 3114 supercontigs<br> 
| 18,561 (Augustus)<br> 
| [ftp://ftp.wormbase.org/pub/wormbase/genomes/brugia/ WormBase]<br> 
| [http://www.wormbase.org/db/seq/gbrowse/brugia/ WormBase]<br>
|-
| ''Heterorhabditis''<br> 
| * in progress *<br> 
| <br> 
| <br> 
| <br> 
| <br>
|-
| ''T. spiralis''<br> 
| * in progress *<br> 
| <br> 
| <br> 
| <br> 
| <br>
|}

<br> 

'''NOTE: '''Gene counts are very sensitive to the methods used for the prediction as well as the quality of the assembly; the numbers shown represent the best guesses based on the results of the [[NGASP|NGASP gene prediction competition]]. Due to significant residual heterozygosity in the ''C. remanei ''and ''C. brenneri'' samples, the assembly sizes of these genomes are inflated by roughly 10 and 30% respectively (Eric Haag, personal communication), and the gene predictions are likely inflated by similar amounts.<br> 

Nematode annotations and a multiz six-way whole genome nematode alignment (''C. elegans, C. briggsae, C. brenneri, C. remanei, C. japonica and P. pacificus) ''are available at the [http://genome.ucsc.edu/cgi-bin/hgTracks?db=ce6 UCSC Genome Browser.] 

<br> 
<pre>               --------------------- C. elegans
               |
               |
          -----|     --------------- C. brenneri
          |    |     |
          |    |     |
          |    |-----|
          |          |     --------- C. remanei
          |          |     |
     -----|          ------|
     |    |                |
     |    |                --------- C. briggsae
     |    |
 ----|    |
|    |    |------------------------- C. japonica
|    |
|    |
|    |------------------------------ P. pacificus
|
|
|----------------------------------- B.malayi
</pre> 
Simplified phylogeny, taken from [http://www.wormbook.org/chapters/www_phylogrhabditids/phylorhab.html The phylogenetic relationships of Caenorhabditis and other rhabditids] (Kiontke and Fitch, 2005)<br> 

= ''C. elegans&nbsp;''Isolate Sequencing Efforts  =

Several groups are resequencing ''C. elegans'' isolates for the purpose of identifying SNPs, characterizing the ''C. elegans'' population structure, or studying how spontaneous mutations arise in laboratory populations. More information is available in [[Nematode resequencing and diversity|Nematode Resequencing and Diversity]].<br> 

<br> 

{| cellspacing="1" cellpadding="1" border="1" width="80%"
|-
| style="text-align: center;" | '''Strain'''<br> 
| style="text-align: center;" | '''Design'''<br> 
| style="text-align: center;" | '''Status'''<br> 
| style="text-align: center;" | '''Download'''<br> 
| style="text-align: center;" | '''Contact'''<br>
|-
| [http://www.wormbase.org/db/gene/strain?name=CB4858;class=Strain CB4858]<br> 
| 9x Solexa<br> 
| [http://www.nature.com/nmeth/journal/v5/n2/full/nmeth.1179.html Published]<br> 
| 50906 SNPs in [http://www.wormbase.org WormBase], access via [http://www.wormbase.org/biomart/martview MartView] by searching for variants in CB4858.<br> 
| [mailto:lhillier@watson.wustl.edu LaDeana Hillier]<br>
|-
| [http://www.wormbase.org/db/get?class=Strain;name=N2 N2] (Bristol)<br> 
| 20x Solexa <br> 
| [http://www.nature.com/nmeth/journal/v5/n2/abs/nmeth.1179.html Published]<br> 
| 1,396 putative SNPs relative to reference N2 strain; 2,082 putative strain-specific indels. Available from publication in supplementary data.<br> 
| [mailto:lhillier@watson.wustl.edu LaDeana Hillier]<br><br>
|-
| [http://www.wormbase.org/db/get?class=Strain;name=JU258 JU258] (Madeira, Portugal)<br> 
| 5.5x Solexa<br> 
| In analysis<br> 
| Raw solexa [ftp://ftp.wormbase.org/pub/wormbase/wormbase_seq/JU258/JU258_solexa_raw.tgz reads] and [ftp://ftp.wormbase.org/pub/wormbase/wormbase_seq/JU258/JU258.snp SNPs] data available at Wormbase ftp. WARNING! These are old SNP calls, many of which have been reported to be false-positives.<br> 
| [mailto:lstein@cshl.edu Lincoln Stein], [mailto:Acutter@eeb.utoronto.ca Asher Cutter], [mailto:kanapin@cshl.edu Alex Kanapin] <br>
|-
| [http://www.wormbase.org/db/get?class=Strain;name=AB1 AB1] (Australia)<br> 
| 6.3x Solexa<br> 
| In analysis<br> 
| Raw solexa [ftp://ftp.wormbase.org/pub/wormbase/wormbase_seq/AB1/AB1_solexa_raw.tgz reads] and [ftp://ftp.wormbase.org/pub/wormbase/wormbase_seq/AB1/AB1.snp SNPs] data available at Wormbase ftp. WARNING! These are old SNP calls, many of which have been reported to be false-positives.<br> 
| 
[mailto:lstein@cshl.edu Lincoln Stein], [mailto:acutter@eeb.utoronto.ca Asher Cutter], [mailto:Felix@ijm.jussieu.fr Marie-Anne Felix], [mailto:kanapin@cshl.edu Alex Kanapin] 

|-
| [http://www.wormbase.org/db/get?class=Strain;name=ED3040 ED3040] (Johannesburg, SA) 
| 6.2x Solexa 
| In analysis 
|  Raw solexa [ftp://ftp.wormbase.org/pub/wormbase/wormbase_seq/ED3040/ED3040_solexa_raw.tgz reads] and [ftp://ftp.wormbase.org/pub/wormbase/wormbase_seq/ED3040/ED3040.snp SNPs] data available at Wormbase ftp. WARNING! These are old SNP calls, many of which have been reported to be false-positives.<br>
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter], [mailto:kanapin@cshl.edu Alex Kanapin]
|-
| [http://www.wormbase.org/db/get?class=Strain;name=MY2 MY2] (Roxel, Germany) 
| 6.2x Solexa 
| Cancelled 
| not available 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
|-
| [http://www.wormbase.org/db/get?class=Strain;name=MY6 MY6] (Roxel, Germany) 
| 6.2x Solexa 
| Cancelled 
| not available 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
|-
| [http://www.wormbase.org/db/get?class=Strain;name=JU322 JU322] (Merlet, France) 
| 6.2x Solexa 
| Cancelled 
| not available 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
|-
| [http://www.wormbase.org/db/get?class=Strain;name=KR314 KR314] (Vancouver, BC, Canada) 
| 6.2x Solexa 
| Cancelled 
| not available 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
|-
| [http://www.wormbase.org/db/get?class=Strain;name=CB4857 CB4857] (Claremont, CA) 
| 6.2x Solexa 
| Cancelled 
| not available 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
|-
| [http://www.wormbase.org/db/get?class=Strain;name=MY3 MY3] (Roxel, Germany) 
| 6.2x Solexa 
| In analysis
| Raw solexa [ftp://ftp.wormbase.org/pub/wormbase/wormbase_seq/MY3/MY3_solexa_raw.tgz reads] and [ftp://ftp.wormbase.org/pub/wormbase/wormbase_seq/MY3/MY3.snp SNPs] data available at Wormbase ftp. WARNING! These are old SNP calls, many of which have been reported to be false-positives.<br> 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter], [mailto:kanapin@cshl.edu Alex Kanapin]
|-
| [http://www.wormbase.org/db/get?class=Strain;name=DR1350 DR1350] (Pasadena, CA) 
| 6.2x Solexa 
| Cancelled 
| not available 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
|-
| [http://www.wormbase.org/db/get?class=Strain;name=PS2025 PS2025] (Altadena, CA) 
| 6.2x Solexa 
| Cancelled 
| not available 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
|-
| [http://www.wormbase.org/db/get?class=Strain;name=ED3051 ED3051] (Ceres, SA) 
| 6.2x Solexa 
| Cancelled 
| not available  
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
|-
| [http://www.wormbase.org/db/get?class=Strain;name=ED3076 ED3076] (Limuru, Kenya) 
| 6.2x Solexa 
| Cancelled 
| not available 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
|-
| [http://www.wormbase.org/db/get?class=Strain;name=CB4856 CB4856] (Hawaii) 
| 5-7x Solexa 
| Unknown 
| <br> 
| [mailto:mmarra@bcgsc.ca Marco Marra]
|}

<br>

= ''Caenorhabditis spp. ''Transcriptome Sequencing Efforts  =

Several groups are resequencing transcriptomes of <span style="font-style: italic;">Caenorhabditis</span> isolates. More information is available in [[Nematode resequencing and diversity|Nematode Resequencing and Diversity]].<br> 

<br> 

{| cellspacing="1" cellpadding="1" border="1" width="80%"
|-
| style="text-align: center;" | '''Strain'''<br> 
| style="text-align: center;" | '''Design'''<br> 
| style="text-align: center;" | '''Status'''<br> 
| style="text-align: center;" | '''Download'''<br> 
| style="text-align: center;" | '''Contact'''<br>
|-
| [http://www.wormbase.org/db/get?class=Strain;name=JU1202 JU1202 (C. sp. 5)]<br> 
| mixed stage/sex cDNA library (1 lane paired-end Solexa)<br> 
| In analysis<br> 
| not yet available 
| 
[mailto:asher.cutter@utoronto.ca Asher Cutter] 

|-
| [http://www.wormbase.org/db/get?class=Strain;name=JU1422 JU1422 (C. sp. 9)]<br> 
| mixed stage/sex cDNA library, L4/young adult female cDNA library, male cDNA library (each 1 lane paired-end Solexa) 
| In analysis
| not yet available 
| [mailto:asher.cutter@utoronto.ca Asher Cutter]
|-
| C. remanei<br> 
| Solexa 
| Unknown 
| <br> 
| [mailto:ehaag@umd.edu Eric Haag]
|}