Difference between revisions of "Nematode sequencing summary"

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This page summarizes the sequencing efforts on nematode genomes. It is a work in progress and is not definitive.<br>  
 
This page summarizes the sequencing efforts on nematode genomes. It is a work in progress and is not definitive.<br>  
  
'''Last update: 13 June 2008'''<br>
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'''Last update: 13 June 2008'''<br>  
  
= Genome Sequencing Efforts<br> =
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= Genome Sequencing Efforts<br> =
  
 
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'''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|NGASP gene prediction competition]].<br>
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'''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|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.<br>  
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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 [http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=108589413&clade=worm&org=0&db=0 UCSC Genome Browser.] A six-way whole genome alignment that adds ''C. japonica'' will be available in July 2008.
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= ''C. elegans&nbsp;''Isolate Sequencing Efforts =
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Several groups are in the process of resequencing ''C. elegans'' isolates for the purpose of identifying SNPs, characterizing the ''C. elegans'' population structure, and/or studying patterns of mutations....

Revision as of 19:37, 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 in the process of resequencing C. elegans isolates for the purpose of identifying SNPs, characterizing the C. elegans population structure, and/or studying patterns of mutations....