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

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