View source for 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. 

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== Solexa Resequencing of Wild C. elegans Isolates  ==

;Rationale 
:Understanding natural population genomic variation iin C. elegans.&nbsp; 
;Source material 
:''C. elegans'' isolates from a variety geographic locations.

{| cellspacing="1" cellpadding="1" border="1" width="80%"
|-
| style="text-align: center;" | '''Strain'''<br> 
| style="text-align: center;" | '''Design'''<br> 
| style="text-align: center;" | '''Status'''<br> 
| style="text-align: center;" | '''Download'''<br> 
| style="text-align: center;" | '''Contact'''<br>
|-
| [http://www.wormbase.org/db/get?class=Strain;name=JU258 JU258] (Madeira, Portugal)<br> 
| 5.5x Solexa<br> 
| In analysis<br> 
| not yet available<br> 
| [mailto:lstein@cshl.edu Lincoln Stein], [mailto:Acutter@eeb.utoronto.ca Asher Cutter]<br>
|-
| [http://www.wormbase.org/db/get?class=Strain;name=AB1 AB1] (Australia)<br> 
| 6.3x Solexa<br> 
| In analysis<br> 
| not yet available 
| 
[mailto:lstein@cshl.edu Lincoln Stein], [mailto:acutter@eeb.utoronto.ca Asher Cutter], [mailto:Felix@ijm.jussieu.fr Marie-Anne Felix] 

|-
| [http://www.wormbase.org/db/get?class=Strain;name=ED3040 ED3040] (Johannesburg, SA) 
| 6.2x Solexa 
| Complete (6.2x) 
| In analysis 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
|-
| [http://www.wormbase.org/db/get?class=Strain;name=MY2 MY2] (Roxel, Germany) 
| Solexa 
| Cancelled 
| not available 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
|-
| [http://www.wormbase.org/db/get?class=Strain;name=MY6 MY6] (Roxel, Germany) 
| Solexa 
| Cancelled 
| not available 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
|-
| [http://www.wormbase.org/db/get?class=Strain;name=JU322 JU322] (Merlet, France) 
| Solexa 
| Cancelled 
| not available 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
|-
| [http://www.wormbase.org/db/get?class=Strain;name=KR314 KR314] (Vancouver, BC, Canada) 
| Solexa 
| Cancelled 
| not available 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
|-
| [http://www.wormbase.org/db/get?class=Strain;name=CB4857 CB4857] (Claremont, CA) 
| Solexa 
| Cancelled 
| not available 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
|-
| [http://www.wormbase.org/db/get?class=Strain;name=MY3 MY3] (Roxel, Germany) 
| Solexa + AB SOLiD 
| Complete (6.2x)
| In analysis 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
|-
| [http://www.wormbase.org/db/get?class=Strain;name=DR1350 DR1350] (Pasadena, CA) 
| Solexa 
| Cancelled 
| not available 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
|-
| [http://www.wormbase.org/db/get?class=Strain;name=PS2025 PS2025] (Altadena, CA) 
| Solexa 
| Cancelled 
| not available 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
|-
| [http://www.wormbase.org/db/get?class=Strain;name=ED3051 ED3051] (Ceres, SA) 
| Solexa 
| Cancelled 
| not available 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
|-
| [http://www.wormbase.org/db/get?class=Strain;name=ED3076 ED3076] (Limuru, Kenya) 
| Solexa 
| Cancelled 
| not available 
| [mailto:lstein@cshl.edu Lincoln Stein],[mailto:acutter@eeb.utoronto.ca Asher Cutter]
|}

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;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 
:[[User:Lstein|Lincoln Stein]] 
:[[User:Asher Cutter|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|CB4858]] (fify-eight) 
;Technology 
:Solexa sequencing, roughly 7x coverage 
;Status 
:Complete 
;Contact 
:[[Elaine Mardis|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|CB4856]] (Hawaiian) 
;Technology 
:Solexa sequencing, 5-7x coverage

Status 

:In progress, data coming in as of 7/10/2007. 
;Contact 
:[[Marco Marra|Marco Marra]], University of British Columbia

== Solexa Resequencing of ''C. elegans'' PB306  ==

;Rationale 
:''missing'' 
;Source material 
:[[PB306|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|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|DR1350]] (a PA3 derivative) and [[N2|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. <br> 
;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)<br> 
;Contact 
:[[Mark Blaxter|Mark Blaxter]], University of Edinburgh, UK<br>

;: 

== 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  ==

<span style="font-size: medium;">Sequencing of new ''Caenorhabditis ''species</span><br><br>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. The Priority Group 1 species sequencing has been funded (October 2008). <br><br>Priority Group 1:<br>'''''Caenorhabditis'' sp. 9 (JU1325)<br>''Caenorhabditis'' sp. 11 (JU1373)<br>''Caenorhabditis ''sp. 7 (JU1199)'''<br><br>[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.]<br> 

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== Other information: C. spp. Transcriptome Sequencing  ==

<span style="font-size: medium;">Transcriptome Sequencing of Non-elegans Caenorhabditis</span><br><br>Several groups are using short-read sequencing on transcriptomes of Caenorhabditis species. 

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

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