Difference between revisions of "Nematode sequencing summary"

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= ''C. elegans ''Isolate Sequencing Efforts  =
 
= ''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.<br>
+
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.<br>  
  
<br>
+
<br>  
  
 
{| width="80%" cellspacing="1" cellpadding="1" border="1"
 
{| width="80%" cellspacing="1" cellpadding="1" border="1"
 
|-
 
|-
| style="text-align: center;" | '''Strain'''<br>
+
| style="text-align: center;" | '''Strain'''<br>  
| style="text-align: center;" | '''Design'''<br>
+
| style="text-align: center;" | '''Design'''<br>  
| style="text-align: center;" | '''Status'''<br>
+
| style="text-align: center;" | '''Status'''<br>  
| style="text-align: center;" | '''Download'''<br>
+
| style="text-align: center;" | '''Download'''<br>  
 
| style="text-align: center;" | '''Contact'''<br>
 
| style="text-align: center;" | '''Contact'''<br>
 
|-
 
|-
| [http://www.wormbase.org/db/gene/strain?name=CB4858;class=Strain CB4858]<br>
+
| [http://www.wormbase.org/db/gene/strain?name=CB4858;class=Strain CB4858]<br>  
| 2.5x Solexa sequencing<br>
+
| 9x Solexa<br>  
| [http://www.nature.com/nmeth/journal/v5/n2/full/nmeth.1179.html Published]<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>
+
| 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>
 
| [mailto:lhillier@watson.wustl.edu LaDeana Hillier]<br>
 
|-
 
|-
| N2 bristol<br>
+
| [http://www.wormbase.org/db/get?class=Strain;name=N2 N2] (Bristol)<br>
| <br>
+
| 20x Solexa <br>
| <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>
 +
| not yet available<br>
 +
| [mailto:lstein@cshl.edu Lincoln Stein], [[acutter@eeb.utoronto.ca|Asher Cutter]]<br>
 +
|-
 +
| [http://www.wormbase.org/db/get?class=Strain;name=AB1 AB1] (Australia)<br>
 +
| 6.3x Solexa<br>  
 +
| In analysis<br>  
 +
| not yet available<br>  
 
|  
 
|  
| <br>
+
[mailto:lstein@cshl.edu Lincoln Stein], [[acutter@eeb.utoronto.ca|Asher Cutter]],
 +
 
 +
[[felix@ijm.jussieu.fr|Marie-Anne Felix]]
 +
 
 
|-
 
|-
| <br>
+
| [http://www.wormbase.org/db/get?class=Strain;name=ED3040 ED3040] (Johannesburg, SA)
| <br>
+
| 6.2x Solexa
| <br>
+
| In analysis
| [http://www.wormbase.org/db/gene/strain?name=N2;class=Strain <br>]
+
| not yet available
| <br>
+
| [mailto:lstein@cshl.edu Lincoln Stein], [[acutter@eeb.utoronto.ca|Asher Cutter]]
 
|-
 
|-
| <br>
+
| [http://www.wormbase.org/db/get?class=Strain;name=CB4856 CB4856] (Hawaii)
| <br>
+
| 5-7x Solexa
| <br>
+
| Unknown
| [http://www.wormbase.org/db/gene/strain?name=N2;class=Strain <br>]
+
|
| <br>
+
| [[mmarra@bcgsc.ca|Marco Marra]]
 
|}
 
|}

Revision as of 22:58, 13 June 2008

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
C. briggsae
10x draft; Annotated
101 Mb in 6 chromosomes, 7 Mb unassigned
21,558 (Jigsaw)
WormBase
WormBase
C. brenneri 9.5x draft, initial gene calls
191 Mb in 3510 supercontigs
30,557 (Jigsaw)
WormBase
WormBase
C. japonica 6.3x draft, initial gene calls
152 Mb in 4657 supercontigs
15,191 (MGENE)
WormBase
WormBase
C. remanei 9.2x draft, initial gene calls
145 Mb in 3670 supercontigs
31,641 (Jigsaw)
WormBase
WormBase
P. pacificus 8.9x draft, initial gene calls
169 Mb in 5106 supercontigs
29,201 (SNAP)
WashU
www.pristionchus.org
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 five-way whole genome nematode alignment (C. elegans, C. briggsae, C. brenneri, C. remanei and P. pacificus) are available at the UCSC Genome Browser. A six-way whole genome alignment that adds C. japonica will be available in July 2008.

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.


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
not yet available
Lincoln Stein, Asher Cutter
AB1 (Australia)
6.3x Solexa
In analysis
not yet available

Lincoln Stein, Asher Cutter,

Marie-Anne Felix

ED3040 (Johannesburg, SA) 6.2x Solexa In analysis not yet available Lincoln Stein, Asher Cutter
CB4856 (Hawaii) 5-7x Solexa Unknown Marco Marra