Difference between revisions of "Nematode resequencing and diversity"

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: [[Dee Denver]], Oregon State U.
 
: [[Dee Denver]], Oregon State U.
  
== Other Information ==
+
== Other Information ==
  
(This is quoted from a letter from Marie-Anne Felix dated April 11, 2007; it is a placeholder until this page grows.)
+
(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data, especially sequencing and SNP data from Dee Denver, Elie Dolgin, Asher Cutter and Matt Rockman (most data are unpublished), it seems that a consensus for resequencing C. elegans isolates is something like the following, in decreasing order of priority:
+
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data, especially sequencing and SNP data from Dee Denver, Elie Dolgin, Asher Cutter and Matt Rockman (most data are unpublished), it seems that a consensus for resequencing C. elegans isolates is something like the following, in decreasing order of priority:  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).
+
*CB4856/Hawaii is apparently being done by Waterston (info by Jim Thomas).  
* JU258 Madeira
+
*JU258 Madeira  
* MY2 Germany
+
*MY2 Germany  
* KR314 Vancouver, BC, Canada
+
*KR314 Vancouver, BC, Canada  
* MY6 Germany
+
*MY6 Germany  
* AB1 Australia
+
*AB1 Australia  
* PB306 N America (exact origin unknown)
+
*PB306 N America (exact origin unknown)  
* ED3040 South Africa
+
*ED3040 South Africa  
* PS2025 Altadena, CA, USA
+
*PS2025 Altadena, CA, USA  
* MY3 Germany
+
*MY3 Germany  
* JU322 France
+
*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)
+
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).
+
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.
+
Apparently Andy Fraser at the Sanger is also planning to do some resequencing, so it may be good that you coordinate the efforts.  
  
<br />
+
<br>
 
 
<span style="font-size: larger;"><u>Sequencing of new ''Caenorhabditis ''species</u></span><u>'''<br>'''</u>
 
 
 
<u></u><span style="font-size: larger;"></span>
 
 
 
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&nbsp; 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 17:51, 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.


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.