Difference between revisions of "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.
+
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.  
  
 +
<br>
  
== Solexa Resequencing of two Wild C. elegans Isolates ==
+
== Solexa Resequencing of Wild C. elegans Isolates ==
  
; Rationale
+
;Rationale  
: Understanding natural population structure in C. elegans. This is a pilot for a larger study.
+
:Understanding natural population genomic variation iin C. elegans.&nbsp;
; Source material
+
;Source material  
: Two ''C. elegans'' isolates isolated from geographically distinct locations.
+
:''C. elegans'' isolates from a variety geographic 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
 
: We expect to have the data sometime during the summer of 2007. Contact one of us for information
 
  
about availability.
+
{| 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]
  
; Contact
+
|-
: [[User:Lstein|Lincoln Stein]]
+
| [http://www.wormbase.org/db/get?class=Strain;name=ED3040 ED3040] (Johannesburg, SA)
: [[User:Asher_Cutter|Asher Cutter]]
+
| 6.2x Solexa
 +
| In analysis
 +
| not yet available
 +
| [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
 +
| In analysis
 +
| not yet available
 +
| [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]
 +
|}
  
== Solexa Resequencing of ''C. elegans'' CB4858 ==
+
<br>
  
; Rationale
+
;Technology  
: Get a strain other than CB4856 for SNP mapping, for behavioral (or other) phenotypes that cannot be mapped using CB4856.
+
:Mostly Solexa/Illumina sequencing. Roughly 5-7x coverage.
; Source material
+
;Data Release
: [[CB4858]] (fify-eight)
+
: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.
; Technology
 
: Solexa sequencing, roughly 7x coverage
 
; Status
 
: Complete
 
; Contact
 
: [[Elaine Mardis]], Washington University Genome Sequencing Center, St. Louis
 
  
== Solexa Resequencing of ''C. elegans'' CB4856 ==
+
;Contact
 +
:[[User:Lstein|Lincoln Stein]]
 +
:[[User:Asher Cutter|Asher Cutter]]
  
; Rationale
+
== Solexa Resequencing of ''C. elegans'' CB4858  ==
: 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
 +
: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
  
; Rationale
+
== Solexa Resequencing of ''C. elegans'' CB4856  ==
: ''missing''
 
; Source material
 
: [/wiki/index.php?title=PB306&action=edit PB306] (North America)
 
; Technology
 
: Solexa sequencing
 
; Status
 
: 5x coverage complete, as of April 2007.
 
; Contact
 
: [/wiki/index.php?title=Dee_Denver&action=edit Dee Denver], Oregon State U.
 
  
== Other Information ==
+
;Rationale
 +
:Source of SNPs for behavioral (or other) phenotypes.
 +
;Source material
 +
:[[CB4856|CB4856]] (Hawaiian)
 +
;Technology
 +
:Solexa sequencing, 5-7x coverage
  
(This is quoted from a letter from Marie-Anne Felix dated April 11, 2007; it is a placeholder until this page grows.)
+
Status
  
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:
+
:In progress, data coming in as of 7/10/2007.  
 +
;Contact
 +
:[[Marco Marra|Marco Marra]], University of British Columbia
  
* CB4856/Hawaii is apparently being done by Waterston (info by Jim Thomas).
+
== Solexa Resequencing of ''C. elegans'' PB306 ==
* 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)
+
;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.
  
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).
+
== Solexa Resequencing of ''C. elegans'' N2 and ''C. elegans'' DR1350  ==
  
Apparently Andy Fraser at the Sanger is also planning to do some resequencing, so it may be good that you coordinate the efforts.
+
;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>
  
<br />
+
;:
  
== Sequencing of ''Caenorhabditis'' sp. 5 JU800 (application) ==
+
== Other Information  ==
  
'''Rationale'''
+
(This is quoted from a letter from Marie-Anne Felix dated April 11, 2007; it is a placeholder until this page grows.)
  
''Caenorhabditis'' sp. 5 is a male-female species that is (currently) the sister species of ''C. briggsae''. The nucleotide turnover is not saturated between the two species, and having both genomes would be helpful for molecular evolution studies. The ''C.'' sp. 5 genome would also add power to the annotation of the ''C. elegans'' genome using comparative data.
+
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:
  
'''Source material'''
+
*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
  
JU800 is derived from JU727 by 20 rounds of inbreeding.
+
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)
  
'''Status/technology'''
+
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).
  
An application to the Genoscope, the French Genome Center, has been submitted by M.A. Félix in April 2007 (answer September 07) for sequencing of the ''Caenorhabditis'' sp. 5 genome:
+
== Other information: C. spp. Genome Sequencing  ==
  
- Sanger sequencing (9-fold coverage) using short insert plasmids and large insert clones (fosmids)
+
<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>
  
- cDNA sequencing using 454 technology (2 million reads) that would help gene annotation and genome assembly.
+
<br>
  
'''Contact'''
+
== Other information: C. spp. Transcriptome Sequencing  ==
  
M.-A. Félix (felix@ijm.jussieu.fr)
+
<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.  
 +
 
 +
<br>
 +
 
 +
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>
 +
 
 +
<br>
 +
 
 +
 
 +
[[Category:User Guide]]
 +
[[Category:Curation]]

Latest revision as of 17:55, 16 August 2010

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.