Difference between revisions of "Nematode sequencing summary"

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Line 19: Line 19:
 
| 101 Mb in 6 chromosomes<br>  
 
| 101 Mb in 6 chromosomes<br>  
 
| 20,177 (curated)<br>  
 
| 20,177 (curated)<br>  
| [ftp://ftp.wormbase.org/pub/wormbase/genomes/elegans/ WormBase]<br>  
+
| [ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/ WormBase]<br>  
 
|  
 
|  
[http://www.wormbase.org/db/seq/gbrowse/elegans/ WormBase]  
+
[http://www.wormbase.org/tools/genome/gbrowse/c_elegans/ WormBase]  
  
 
[http://genome.ucsc.edu/cgi-bin/hgTracks?db=ce6 UCSC]  
 
[http://genome.ucsc.edu/cgi-bin/hgTracks?db=ce6 UCSC]  
Line 30: Line 30:
 
| 101 Mb in 6 chromosomes, 7 Mb unassigned<br>  
 
| 101 Mb in 6 chromosomes, 7 Mb unassigned<br>  
 
| 21,558 (Jigsaw)<br>  
 
| 21,558 (Jigsaw)<br>  
| [ftp://ftp.wormbase.org/pub/wormbase/genomes/briggsae/ WormBase]<br>  
+
| [ftp://ftp.wormbase.org/pub/wormbase/species/c_briggsae/ WormBase]<br>  
 
|  
 
|  
[http://www.wormbase.org/db/seq/gbrowse/briggsae/ WormBase]  
+
[http://www.wormbase.org/tools/genome/gbrowse/c_briggsae/ WormBase]  
  
 
[http://genome.ucsc.edu/cgi-bin/hgTracks?db=cb3 UCSC]  
 
[http://genome.ucsc.edu/cgi-bin/hgTracks?db=cb3 UCSC]  
Line 41: Line 41:
 
| 191 Mb in 3510 supercontigs<br>  
 
| 191 Mb in 3510 supercontigs<br>  
 
| 30,557 (Jigsaw)<br>  
 
| 30,557 (Jigsaw)<br>  
| [ftp://ftp.wormbase.org/pub/wormbase/genomes/brenneri/ WormBase]<br>  
+
| [ftp://ftp.wormbase.org/pub/wormbase/species/c_brenneri/ WormBase]<br>  
 
|  
 
|  
[http://www.wormbase.org/db/seq/gbrowse/brenneri/ WormBase]  
+
[http://www.wormbase.org/tools/genome/gbrowse/c_brenneri/ WormBase]  
  
 
[http://genome.ucsc.edu/cgi-bin/hgTracks?db=caePb2 UCSC]  
 
[http://genome.ucsc.edu/cgi-bin/hgTracks?db=caePb2 UCSC]  
Line 52: Line 52:
 
| 152 Mb in 4657 supercontigs<br>  
 
| 152 Mb in 4657 supercontigs<br>  
 
| 15,191 (MGENE)<br>  
 
| 15,191 (MGENE)<br>  
| [ftp://ftp.wormbase.org/pub/wormbase/genomes/japonica/ WormBase]<br>  
+
| [ftp://ftp.wormbase.org/pub/wormbase/species/c_japonica/ WormBase]<br>  
 
|  
 
|  
[http://www.wormbase.org/db/seq/gbrowse/japonica/ WormBase]  
+
[http://www.wormbase.org/tools/genome/gbrowse/c_japonica/ WormBase]  
  
 
[http://genome.ucsc.edu/cgi-bin/hgTracks?db=caeJap1 UCSC]  
 
[http://genome.ucsc.edu/cgi-bin/hgTracks?db=caeJap1 UCSC]  
Line 63: Line 63:
 
| 145 Mb in 3670 supercontigs<br>  
 
| 145 Mb in 3670 supercontigs<br>  
 
| 31,641 (Jigsaw)<br>  
 
| 31,641 (Jigsaw)<br>  
| [ftp://ftp.wormbase.org/pub/wormbase/genomes/remanei/ WormBase]<br>  
+
| [ftp://ftp.wormbase.org/pub/wormbase/species/c_remanei/ WormBase]<br>  
 
|  
 
|  
[http://www.wormbase.org/db/seq/gbrowse/remanei/ WormBase]  
+
[http://www.wormbase.org/tools/genome/gbrowse/c_remanei/ WormBase]  
  
 
[http://genome.ucsc.edu/cgi-bin/hgTracks?db=caeRem3 UCSC]  
 
[http://genome.ucsc.edu/cgi-bin/hgTracks?db=caeRem3 UCSC]  
Line 85: Line 85:
 
| 72 Mb in 3114 supercontigs<br>  
 
| 72 Mb in 3114 supercontigs<br>  
 
| 18,561 (Augustus)<br>  
 
| 18,561 (Augustus)<br>  
| [ftp://ftp.wormbase.org/pub/wormbase/genomes/brugia/ WormBase]<br>  
+
| [ftp://ftp.wormbase.org/pub/wormbase/species/b_malayi/ WormBase]<br>  
| [http://www.wormbase.org/db/seq/gbrowse/brugia/ WormBase]<br>
+
| [http://www.wormbase.org/tools/genome/gbrowse/b_malayi/ WormBase]<br>
 
|-
 
|-
 
| ''Heterorhabditis''<br>  
 
| ''Heterorhabditis''<br>  
Line 132: Line 132:
 
|----------------------------------- B.malayi
 
|----------------------------------- B.malayi
 
</pre>  
 
</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>  
+
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  =
 
= ''C. elegans&nbsp;''Isolate Sequencing Efforts  =
Line 163: Line 163:
 
| 5.5x Solexa<br>  
 
| 5.5x Solexa<br>  
 
| In analysis<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.<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>
 
| [mailto:lstein@cshl.edu Lincoln Stein], [mailto:Acutter@eeb.utoronto.ca Asher Cutter], [mailto:kanapin@cshl.edu Alex Kanapin] <br>
 
|-
 
|-
Line 182: Line 182:
 
| [http://www.wormbase.org/db/get?class=Strain;name=MY2 MY2] (Roxel, Germany)  
 
| [http://www.wormbase.org/db/get?class=Strain;name=MY2 MY2] (Roxel, Germany)  
 
| 6.2x Solexa  
 
| 6.2x Solexa  
| In queue
+
| Cancelled
| not yet available  
+
| not available  
 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
 
| [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)  
 
| [http://www.wormbase.org/db/get?class=Strain;name=MY6 MY6] (Roxel, Germany)  
 
| 6.2x Solexa  
 
| 6.2x Solexa  
| In queue
+
| Cancelled
| not yet available  
+
| not available  
 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
 
| [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)  
 
| [http://www.wormbase.org/db/get?class=Strain;name=JU322 JU322] (Merlet, France)  
 
| 6.2x Solexa  
 
| 6.2x Solexa  
| In queue
+
| Cancelled
| not yet available  
+
| not available  
 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
 
| [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)  
 
| [http://www.wormbase.org/db/get?class=Strain;name=KR314 KR314] (Vancouver, BC, Canada)  
 
| 6.2x Solexa  
 
| 6.2x Solexa  
| In queue
+
| Cancelled
| not yet available  
+
| not available  
 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
 
| [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)  
 
| [http://www.wormbase.org/db/get?class=Strain;name=CB4857 CB4857] (Claremont, CA)  
 
| 6.2x Solexa  
 
| 6.2x Solexa  
| In queue
+
| Cancelled
| not yet available  
+
| not available  
 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
 
| [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)  
 
| [http://www.wormbase.org/db/get?class=Strain;name=MY3 MY3] (Roxel, Germany)  
 
| 6.2x Solexa  
 
| 6.2x Solexa  
| In queue
+
| 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>  
 
| 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]
 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter], [mailto:kanapin@cshl.edu Alex Kanapin]
Line 218: Line 218:
 
| [http://www.wormbase.org/db/get?class=Strain;name=DR1350 DR1350] (Pasadena, CA)  
 
| [http://www.wormbase.org/db/get?class=Strain;name=DR1350 DR1350] (Pasadena, CA)  
 
| 6.2x Solexa  
 
| 6.2x Solexa  
| In queue
+
| Cancelled
| not yet available  
+
| not available  
 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
 
| [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)  
 
| [http://www.wormbase.org/db/get?class=Strain;name=PS2025 PS2025] (Altadena, CA)  
 
| 6.2x Solexa  
 
| 6.2x Solexa  
| In queue
+
| Cancelled
| not yet available  
+
| not available  
 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
 
| [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)  
+
| ED3051 (Ceres, SA)  
 
| 6.2x Solexa  
 
| 6.2x Solexa  
| In queue
+
| Cancelled
| not yet available  
+
| not available
 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
 
| [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)  
+
| ED3076 (Limuru, Kenya)  
 
| 6.2x Solexa  
 
| 6.2x Solexa  
| In queue
+
| Cancelled
| not yet available  
+
| not available  
 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
 
|-
 
|-
Line 265: Line 265:
 
| [http://www.wormbase.org/db/get?class=Strain;name=JU1202 JU1202 (C. sp. 5)]<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>  
 
| mixed stage/sex cDNA library (1 lane paired-end Solexa)<br>  
| In queue<br>  
+
| In analysis<br>  
 
| not yet available  
 
| not yet available  
 
|  
 
|  
Line 273: Line 273:
 
| [http://www.wormbase.org/db/get?class=Strain;name=JU1422 JU1422 (C. sp. 9)]<br>  
 
| [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)  
 
| mixed stage/sex cDNA library, L4/young adult female cDNA library, male cDNA library (each 1 lane paired-end Solexa)  
| In queue
+
| In analysis
 
| not yet available  
 
| not yet available  
 
| [mailto:asher.cutter@utoronto.ca Asher Cutter]
 
| [mailto:asher.cutter@utoronto.ca Asher Cutter]
Line 283: Line 283:
 
| [mailto:ehaag@umd.edu Eric Haag]
 
| [mailto:ehaag@umd.edu Eric Haag]
 
|}
 
|}
 +
 +
 +
 +
[[Category:Curation]]
 +
[[Category:User Guide]]

Latest revision as of 13:38, 10 April 2012

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

Last update: 13 June 2008

Genome Sequencing Efforts

Nematode Sequencing Status
Species
Status
Assembly size
Gene count (method)
Download
Browser
C. elegans
finished; Annotated
101 Mb in 6 chromosomes
20,177 (curated)
WormBase

WormBase

UCSC

C. briggsae
10x draft; Annotated
101 Mb in 6 chromosomes, 7 Mb unassigned
21,558 (Jigsaw)
WormBase

WormBase

UCSC

C. brenneri 9.5x draft, initial gene calls
191 Mb in 3510 supercontigs
30,557 (Jigsaw)
WormBase

WormBase

UCSC

C. japonica 6.3x draft, initial gene calls
152 Mb in 4657 supercontigs
15,191 (MGENE)
WormBase

WormBase

UCSC

C. remanei 9.2x draft, initial gene calls
145 Mb in 3670 supercontigs
31,641 (Jigsaw)
WormBase

WormBase

UCSC

P. pacificus 8.9x draft, initial gene calls
169 Mb in 5106 supercontigs
29,201 (SNAP)
WashU

www.pristionchus.org

UCSC

B. malayi 8.9x draft, genes annotated
72 Mb in 3114 supercontigs
18,561 (Augustus)
WormBase
WormBase
Heterorhabditis
* in progress *




T. spiralis
* in progress *





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 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.

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 UCSC Genome Browser.


               --------------------- C. elegans
               |
               |
          -----|     --------------- C. brenneri
          |    |     |
          |    |     |
          |    |-----|
          |          |     --------- C. remanei
          |          |     |
     -----|          ------|
     |    |                |
     |    |                --------- C. briggsae
     |    |
 ----|    |
|    |    |------------------------- C. japonica
|    |
|    |
|    |------------------------------ P. pacificus
|
|
|----------------------------------- B.malayi

Simplified phylogeny, taken from The phylogenetic relationships of Caenorhabditis and other rhabditids (Kiontke and Fitch, 2005)

C. elegans 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.


Strain
Design
Status
Download
Contact
CB4858
9x Solexa
Published
50906 SNPs in WormBase, access via MartView by searching for variants in CB4858.
LaDeana Hillier
N2 (Bristol)
20x Solexa
Published
1,396 putative SNPs relative to reference N2 strain; 2,082 putative strain-specific indels. Available from publication in supplementary data.
LaDeana Hillier

JU258 (Madeira, Portugal)
5.5x Solexa
In analysis
Raw solexa reads and SNPs data available at Wormbase ftp. WARNING! These are old SNP calls, many of which have been reported to be false-positives.
Lincoln Stein, Asher Cutter, Alex Kanapin
AB1 (Australia)
6.3x Solexa
In analysis
Raw solexa reads and SNPs data available at Wormbase ftp. WARNING! These are old SNP calls, many of which have been reported to be false-positives.

Lincoln Stein, Asher Cutter, Marie-Anne Felix, Alex Kanapin

ED3040 (Johannesburg, SA) 6.2x Solexa In analysis Raw solexa reads and SNPs data available at Wormbase ftp. WARNING! These are old SNP calls, many of which have been reported to be false-positives.
Lincoln Stein,Asher Cutter, Alex Kanapin
MY2 (Roxel, Germany) 6.2x Solexa Cancelled not available Lincoln Stein,Asher Cutter
MY6 (Roxel, Germany) 6.2x Solexa Cancelled not available Lincoln Stein,Asher Cutter
JU322 (Merlet, France) 6.2x Solexa Cancelled not available Lincoln Stein,Asher Cutter
KR314 (Vancouver, BC, Canada) 6.2x Solexa Cancelled not available Lincoln Stein,Asher Cutter
CB4857 (Claremont, CA) 6.2x Solexa Cancelled not available Lincoln Stein,Asher Cutter
MY3 (Roxel, Germany) 6.2x Solexa In analysis Raw solexa reads and SNPs data available at Wormbase ftp. WARNING! These are old SNP calls, many of which have been reported to be false-positives.
Lincoln Stein,Asher Cutter, Alex Kanapin
DR1350 (Pasadena, CA) 6.2x Solexa Cancelled not available Lincoln Stein,Asher Cutter
PS2025 (Altadena, CA) 6.2x Solexa Cancelled not available Lincoln Stein,Asher Cutter
ED3051 (Ceres, SA) 6.2x Solexa Cancelled not available Lincoln Stein,Asher Cutter
ED3076 (Limuru, Kenya) 6.2x Solexa Cancelled not available Lincoln Stein,Asher Cutter
CB4856 (Hawaii) 5-7x Solexa Unknown
Marco Marra


Caenorhabditis spp. Transcriptome Sequencing Efforts

Several groups are resequencing transcriptomes of Caenorhabditis isolates. More information is available in Nematode Resequencing and Diversity.


Strain
Design
Status
Download
Contact
JU1202 (C. sp. 5)
mixed stage/sex cDNA library (1 lane paired-end Solexa)
In analysis
not yet available

Asher Cutter

JU1422 (C. sp. 9)
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 Asher Cutter
C. remanei
Solexa Unknown
Eric Haag