Difference between revisions of "Nematode resequencing and diversity"
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| − | = | + | <span style="font-size: larger;"><u>Sequencing of new ''Caenorhabditis ''species</u></span><u>'''<br>'''</u> |
| − | + | <u></u><span style="font-size: larger;"></span> | |
| − | ''Caenorhabditis'' | + | A proposal to sequence up to seven additional genomes and cDNAs of''Caenorhabditis ''species has been submitted to NIH as part of the modENCODE project, organized by Fabio Piano (worms) and Peter Cherbas (flies), with contribution from K. Kiontke, P. Sternberg, R. Waterston, D. Fitch, A. Cutter and M.-A. Félix.<br> |
| − | + | <br> | |
| − | + | Priority Group 1 | |
| − | '' | + | ''Caenorhabditis'' sp. 9 (JU1325) |
| − | + | ''Caenorhabditis'' sp. 11 (JU1373) | |
| − | + | ''Caenorhabditis'' sp. 7 (JU1199) | |
| − | + | <br> | |
| − | + | Priority Group 2 | |
| − | + | ''Caenorhabditis ''sp. 5 (JU727) | |
| − | + | ''Caenorhabditis ''sp. 10 (JU1333) | |
| + | |||
| + | Two species from: ''Caenorhabditis'' sp. 6, ''C.'' sp. 3, ''C. drosophilae'', ''C.'' sp. 8, ''C.'' sp. 2. | ||
Revision as of 14:49, 4 September 2008
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
- Complete as of October 2007. We are running another roughly 5x for each strain to determine the effects of read depth on alignment/assembly quality.
- 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. This run had very high error rates associated with our old Solexa machine's technical problems. We have since received a replacement machine from Illumina that is working much better. We do not plan to re-do PB306, however, until after we have completed sequencing from mutation-accumulation lines.
- 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 new Caenorhabditis species
A proposal to sequence up to seven additional genomes and cDNAs ofCaenorhabditis species has been submitted to NIH as part of the modENCODE project, organized by Fabio Piano (worms) and Peter Cherbas (flies), with contribution from K. Kiontke, P. Sternberg, R. Waterston, D. Fitch, A. Cutter and M.-A. Félix.
Priority Group 1
Caenorhabditis sp. 9 (JU1325)
Caenorhabditis sp. 11 (JU1373)
Caenorhabditis sp. 7 (JU1199)
Priority Group 2
Caenorhabditis sp. 5 (JU727)
Caenorhabditis sp. 10 (JU1333)
Two species from: Caenorhabditis sp. 6, C. sp. 3, C. drosophilae, C. sp. 8, C. sp. 2.
