Difference between revisions of "Nematode resequencing and diversity"

From WormBaseWiki
Jump to navigationJump to search
Line 105: Line 105:
  
 
M.-A. Félix (felix@ijm.jussieu.fr)
 
M.-A. Félix (felix@ijm.jussieu.fr)
 +
 +
October 2007: this application was rejected by the Genoscope.

Revision as of 06:22, 21 October 2007

This is a community page for registering information about future and pending nematode (re)sequencing projects. Please describe briefly the species, population or isolate you will be (re)sequencing, the technology you will be using, the status of the project, and contact information.


Solexa Resequencing of two Wild C. elegans Isolates

Rationale
Understanding natural population structure in C. elegans. This is a pilot for a larger study.
Source material
Two C. elegans isolates isolated from geographically distinct locations.
JU258 (Madeira, Portugal; collected by M.A. Felix)
ED3040 (Johannesburg, South Africa; collected by E. Dolgin).
Technology
Solexa sequencing, 35 cycles. Roughly 5x coverage.
Data Release
Our first attempts ran into technical problems and we are rebuilding the libraries (September 28, 2008). Hopefully data will be available in October 2008.
Contact
Lincoln Stein
Asher Cutter

Solexa Resequencing of C. elegans CB4858

Rationale
Get a strain other than CB4856 for SNP mapping, for behavioral (or other) phenotypes that cannot be mapped using CB4856.
Source material
CB4858 (fify-eight)
Technology
Solexa sequencing, roughly 7x coverage
Status
Complete
Contact
Elaine Mardis, Washington University Genome Sequencing Center, St. Louis

Solexa Resequencing of C. elegans CB4856

Rationale
Source of SNPs for behavioral (or other) phenotypes.
Source material
CB4856 (Hawaiian)
Technology
Solexa sequencing, 5-7x coverage
Status
In progress, data coming in as of 7/10/2007.
Contact
Marco Marra, University of British Columbia

Solexa Resequencing of C. elegans PB306

Rationale
missing
Source material
PB306 (North America)
Technology
Solexa sequencing
Status
5x coverage complete, as of April 2007.
Contact
Dee Denver, Oregon State U.

Other Information

(This is quoted from a letter from Marie-Anne Felix dated April 11, 2007; it is a placeholder until this page grows.)

After a round of e-mailing, taking account of available data, especially sequencing and SNP data from Dee Denver, Elie Dolgin, Asher Cutter and Matt Rockman (most data are unpublished), it seems that a consensus for resequencing C. elegans isolates is something like the following, in decreasing order of priority:

  • CB4856/Hawaii is apparently being done by Waterston (info by Jim Thomas).
  • JU258 Madeira
  • MY2 Germany
  • KR314 Vancouver, BC, Canada
  • MY6 Germany
  • AB1 Australia
  • PB306 N America (exact origin unknown)
  • ED3040 South Africa
  • PS2025 Altadena, CA, USA
  • MY3 Germany
  • JU322 France

I can give a justification for this set if it is of any use. It basically maximizes diversity. It also covers four continents, but basically there is no large-scale geographic structure in the C. elegans species. (just found one elegans strain in Japan, but no sequence data yet)

Tell me if you need any information (like a general rationale for resequencing, or for choosing the strains). I can provide the strains which are not at CGC (I think ED3040 is the only one).

Apparently Andy Fraser at the Sanger is also planning to do some resequencing, so it may be good that you coordinate the efforts.


Sequencing of Caenorhabditis sp. 5 JU800 (application)

Rationale

Caenorhabditis sp. 5 is a male-female species that is (currently) the sister species of C. briggsae. The nucleotide turnover is not saturated between the two species, and having both genomes would be helpful for molecular evolution studies. The C. sp. 5 genome would also add power to the annotation of the C. elegans genome using comparative data.

Source material

JU800 is derived from JU727 by 20 rounds of inbreeding.

Status/technology

An application to the Genoscope, the French Genome Center, has been submitted by M.A. Félix in April 2007 (answer September 07) for sequencing of the Caenorhabditis sp. 5 genome:

- Sanger sequencing (9-fold coverage) using short insert plasmids and large insert clones (fosmids)

- cDNA sequencing using 454 technology (2 million reads) that would help gene annotation and genome assembly.

Contact

M.-A. Félix (felix@ijm.jussieu.fr)

October 2007: this application was rejected by the Genoscope.