Nematode resequencing and diversity

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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 Wild C. elegans Isolates

Rationale
Understanding natural population genomic variation iin C. elegans. 
Source material
C. elegans isolates from a variety geographic locations.
Strain
Design
Status
Download
Contact
JU258 (Madeira, Portugal)
5.5x Solexa
In analysis
not yet available
Lincoln Stein, Asher Cutter
AB1 (Australia)
6.3x Solexa
In analysis
not yet available

Lincoln Stein, Asher Cutter, Marie-Anne Felix

ED3040 (Johannesburg, SA) 6.2x Solexa In analysis not yet available Lincoln Stein,Asher Cutter
MY2 (Roxel, Germany) Solexa Cancelled not available Lincoln Stein,Asher Cutter
MY6 (Roxel, Germany) Solexa Cancelled not available Lincoln Stein,Asher Cutter
JU322 (Merlet, France) Solexa Cancelled not available Lincoln Stein,Asher Cutter
KR314 (Vancouver, BC, Canada) Solexa Cancelled not available Lincoln Stein,Asher Cutter
CB4857 (Claremont, CA) Solexa Cancelled not available Lincoln Stein,Asher Cutter
MY3 (Roxel, Germany) Solexa + AB SOLiD In analysis not yet available Lincoln Stein,Asher Cutter
DR1350 (Pasadena, CA) Solexa Cancelled not available Lincoln Stein,Asher Cutter
PS2025 (Altadena, CA) Solexa Cancelled not available Lincoln Stein,Asher Cutter
ED3051 (Ceres, SA) Solexa Cancelled not available Lincoln Stein,Asher Cutter
ED3076 (Limuru, Kenya) Solexa Cancelled not available Lincoln Stein,Asher Cutter


Technology
Mostly Solexa/Illumina sequencing. Roughly 5-7x 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.

Solexa Resequencing of C. elegans N2 and C. elegans DR1350

Rationale
Mark Viney in Bristol has been mapping quantitative trait loci in recombinant inbred lines between N2 and DR1350. In order to identify the likely quantitative trait nucleotides underpinning the QTL in the RIL crosses, we sequenced DR1350 to ~16 fold depth. As some of the DR1350 genome (large segments of chromosomes) appear to be derived from an N2-like background, we also sequences N2 to 16 fold to affirm single nucleotide polymorphism calls in these regions, and to assess the reliability of indel and SNP calls in the DR1350 data.
Source material
DR1350 (a PA3 derivative) and N2 (Mark Viney's copy of this strain from CGC; we call this N2Viney, as N2Bristol would cause far too much confusion!)
Technology
Solexa sequencing using a GAI instrument, initially with 36 base reads and latterly with 44 base reads.
Status
We aimed for equal coverage over both genomes, and achieved a mean of 14 fold depth. These data were complete as of June 2008; we are currently (Nov 2008) in the process of analysing them. If anyone wants a look see, email me (Mark Blaxter)
Contact
Mark Blaxter, University of Edinburgh, UK

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).

Other information: C. spp. Genome Sequencing

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.]


Other information: C. spp. Transcriptome Sequencing

Transcriptome Sequencing of Non-elegans Caenorhabditis

Several groups are using short-read sequencing on transcriptomes of Caenorhabditis species.


Asher Cutter has generated cDNA libraries for the following species:

  • C. sp. 5 (JU1202) - mixed stage/sex
  • C. sp. 9 (JU1422) - mixed stage/sex, all male, all L4/young adult female

We have paired-end reads for 1 lane/library on the Solexa/Illumina GAII sequencer at the University of Toronto CAGEF. Assembly and analysis is in progress.

Eric Haag has generated Solexa/Illumina data for C. remanei, with analysis in progress.