Difference between revisions of "Nematode resequencing and diversity"
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: Get a strain other than CB4856 for SNP mapping, for behavioral (or other) phenotypes that cannot be mapped using CB4856. | : Get a strain other than CB4856 for SNP mapping, for behavioral (or other) phenotypes that cannot be mapped using CB4856. | ||
; Source material | ; Source material | ||
| − | : [CB4858] (fify-eight) | + | : [[CB4858]] (fify-eight) |
; Technology | ; Technology | ||
: Solexa sequencing, roughly 7x coverage | : Solexa sequencing, roughly 7x coverage | ||
Revision as of 12:09, 28 September 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.
Contents
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
- We expect to have the data sometime during the summer of 2007. Contact one of us for information
about availability.
- 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
- [/wiki/index.php?title=CB4856&action=edit CB4856] (Hawaiian)
- Technology
- Solexa sequencing, 5-7x coverage
- Status
- In progress, data coming in as of 7/10/2007.
- Contact
- [/wiki/index.php?title=Marco_Marra&action=edit Marco Marra], University of British Columbia
Solexa Resequencing of C. elegans PB306
- Rationale
- missing
- Source material
- [/wiki/index.php?title=PB306&action=edit PB306] (North America)
- Technology
- Solexa sequencing
- Status
- 5x coverage complete, as of April 2007.
- Contact
- [/wiki/index.php?title=Dee_Denver&action=edit 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)
