Nematode resequencing and diversity

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

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data, especially sequencing and SNP data from Dee Denver, Elie Dolgin, Asher Cutter and Matt Rockman (most data are unpublished), it seems that a consensus for resequencing C. elegans isolates is something like the following, in decreasing order of priority: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

Sequencing of new Caenorhabditis species

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. The Priority Group 1 species sequencing has been funded (October 2008).

Priority Group 1:
Caenorhabditis sp. 9 (JU1325)
Caenorhabditis sp. 11 (JU1373)
Caenorhabditis sp. 7 (JU1199)

[Priority Group 2 was:Caenorhabditis sp. 5 (JU727), Caenorhabditis sp. 10 (JU1333), two species among: Caenorhabditis sp. 6, C. sp. 3, C. drosophilae, C. sp. 8, C. sp. 2.]