Difference between revisions of "Nematode sequencing summary"
| Line 108: | Line 108: | ||
| 20x Solexa <br> | | 20x Solexa <br> | ||
| [http://www.nature.com/nmeth/journal/v5/n2/abs/nmeth.1179.html Published]<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> | + | | 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> | | [mailto:lhillier@watson.wustl.edu LaDeana Hillier]<br><br> | ||
|- | |- | ||
| Line 115: | Line 115: | ||
| In analysis<br> | | In analysis<br> | ||
| not yet available<br> | | not yet available<br> | ||
| − | | [mailto:lstein@cshl.edu Lincoln Stein], [[ | + | | [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> | | [http://www.wormbase.org/db/get?class=Strain;name=AB1 AB1] (Australia)<br> | ||
| Line 122: | Line 122: | ||
| not yet available<br> | | not yet available<br> | ||
| | | | ||
| − | [mailto:lstein@cshl.edu Lincoln Stein], [ | + | [mailto:lstein@cshl.edu Lincoln Stein], [mailto:acutter@eeb.utoronto.ca Asher Cutter], |
| − | [[ | + | [[Felix@ijm.jussieu.fr|Marie-Anne Felix]] |
|- | |- | ||
| − | | [http://www.wormbase.org/db/get?class=Strain;name=ED3040 ED3040] (Johannesburg, SA) | + | | [http://www.wormbase.org/db/get?class=Strain;name=ED3040 ED3040] (Johannesburg, SA) |
| − | | 6.2x Solexa | + | | 6.2x Solexa |
| − | | In analysis | + | | In analysis |
| − | | not yet available | + | | [mailto:acutter@eeb.utoronto.ca not yet available] |
| − | | [mailto: | + | | [mailto:acutter@eeb.utoronto.ca Lincoln Stein, Asher Cutter] |
|- | |- | ||
| − | | [http://www.wormbase.org/db/get?class=Strain;name=CB4856 CB4856] (Hawaii) | + | | [http://www.wormbase.org/db/get?class=Strain;name=CB4856 CB4856] (Hawaii) |
| − | | 5-7x Solexa | + | | 5-7x Solexa |
| − | | Unknown | + | | Unknown |
| | | | ||
| − | | [ | + | | [mailto:mmarra@bcgsc.ca Marco Marra] |
|} | |} | ||
Revision as of 23:03, 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
| 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 |
|
| ED3040 (Johannesburg, SA) | 6.2x Solexa | In analysis | not yet available | Lincoln Stein, Asher Cutter |
| CB4856 (Hawaii) | 5-7x Solexa | Unknown | Marco Marra |
