Nematode sequencing summary

From WormBaseWiki
Jump to: navigation, search

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