Nematode sequencing summary
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 |
|
| C. briggsae |
10x draft; Annotated |
101 Mb in 6 chromosomes, 7 Mb unassigned |
21,558 (Jigsaw) |
WormBase |
|
| C. brenneri | 9.5x draft, initial gene calls |
191 Mb in 3510 supercontigs |
30,557 (Jigsaw) |
WormBase |
|
| C. japonica | 6.3x draft, initial gene calls |
152 Mb in 4657 supercontigs |
15,191 (MGENE) |
WormBase |
|
| C. remanei | 9.2x draft, initial gene calls |
145 Mb in 3670 supercontigs |
31,641 (Jigsaw) |
WormBase |
|
| P. pacificus | 8.9x draft, initial gene calls |
169 Mb in 5106 supercontigs |
29,201 (SNAP) |
WashU |
|
| 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. |
|
| 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 | In queue | not yet available | Lincoln Stein,Asher Cutter |
| MY6 (Roxel, Germany) | 6.2x Solexa | In queue | not yet available | Lincoln Stein,Asher Cutter |
| JU322 (Merlet, France) | 6.2x Solexa | In queue | not yet available | Lincoln Stein,Asher Cutter |
| KR314 (Vancouver, BC, Canada) | 6.2x Solexa | In queue | not yet available | Lincoln Stein,Asher Cutter |
| CB4857 (Claremont, CA) | 6.2x Solexa | In queue | not yet available | Lincoln Stein,Asher Cutter |
| MY3 (Roxel, Germany) | 6.2x Solexa | In queue | 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 | In queue | not yet available | Lincoln Stein,Asher Cutter |
| PS2025 (Altadena, CA) | 6.2x Solexa | In queue | not yet available | Lincoln Stein,Asher Cutter |
| ED3051 (Ceres, SA) | 6.2x Solexa | In queue | not yet available | Lincoln Stein,Asher Cutter |
| ED3076 (Limuru, Kenya) | 6.2x Solexa | In queue | not yet 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 queue |
not yet available | |
| 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 queue | not yet available | Asher Cutter |
| C. remanei |
Solexa | Unknown | Eric Haag |
