Sequencing

Sequencing Strategy Sequencing Plans and Progress Statistics Why Sequence Them? Information for Collaborators Protocols Genome Portal Site

FY2004 Sequencing for the
DOE Microbial Genome Program

For more information about the DOE Office of Science's Microbial Genome Program, see http://microbialgenomics.energy.gov/. For more information about microbial sequencing at JGI, contact David Bruce. This page is verified at the beginning of every month.

Chlorobia (avg:~2.4Mb)

Organism Status* Public Release** Genome Size
Chlorobium ferrooxidans DSM 13031 In finishing (by collaborator) 7/10/2006 (draft) 2.40 Mb
Chlorobium limicola DSMZ 245 In finishing (by collaborator) 4/8/05 (draft) 2.4 Mb
Chlorobium phaeobacteroides BS1 In finishing (by collaborator) 6/1/05 (draft) 2.4 Mb
Chlorobium phaeobacteroides DSM 266 Finished 12/13/06 2.3 Mb
Pelodictyon luteolum DSMZ 273 Finished 2/18/05 2.3 Mb
Pelodictyon phaeoclathratiforme BU-1 (DSM 5477) In finishing (by collaborator) 2/24/05 (draft) 2.4 Mb
Prosthecochloris aestuarii DSM 271 In finishing (by collaborator) 2/19/05 (draft) 2.4 Mb
Prosthecochloris vibrioformis DSM 265 Finished 4/19/07 2.4 Mb
Chlorobaculum parvum In finishing   n/a
Chloroherpeton thalassium In finishing   n/a

Model Syntrophic Consortium

Organism Status* Public Release ** Genome Size
Syntrophobacter fumaroxidans MPOB Finished 11/6/06 3.3 Mb
Syntrophomonas wolfei Göttingen (DSM 2245B) Finished 9/20/06 3 Mb
Methanospirillum hungatei JF1 Finished 3/1/06 3.70 Mb

Facultative Metal-reducing Gamma proteobacteria

Organism Status* Public Release** Genome Size
Shewanella amazonensis SB2B Finished 1/8/2007 4.40 Mb
Shewanella baltica OS155 Finished 2/28/2007 5.20 Mb
Shewanella baltica OS185 Finished 7/18/2007  
Shewanella denitrificans OS217 Finished 4/12/2006 4.70 Mb
Shewanella frigidimarina NCIMB 400 Finished 9/20/2006 4.90 Mb
Shewanella putrefaciens 200 In finishing (LLNL) 1/31/2007 (draft) 4.5 Mb
Shewanella putrefaciens CN-32 Finished 5/9/2007 4.5 Mb
Shewanella loihica PV-4 Finished 3/19/2007 4.5 Mb

Five bacteria involved in nitrification

Organism Status* Public Release** Genome Size
Nitrobacter hamburgensis X14 Finished 4/19/06 5.011530 Mb
Nitrobacter winogradskyi Nb-255 Finished 5/13/05 3.40 Mb
Nitrosococcus oceani ATCC 19707 Finished 5/13/05 3.5 Mb
Nitrosomonas eutropha C71 Finished 9/13/06 2.70 Mb
Nitrosospira multiformis ATCC 25196 Finished 1/9/05 3.20 Mb

Single microbes

Organism Status* Public Release** Genome Size
Alkaliphilus metalliredigenes QYMF Finished 7/9/2007 4.5 Mb
Anaeromyxobacter dehalogenans 2CP-C Finished 2/26/05 5.20 Mb
Arthrobacter sp. FB24 Finished 11/6/06 5.20 Mb
Bath hot springs metagenome and thermophages Y4.1MC1, Y4.1MC4, and Y5.1MC23 Y4.1MC4 pending, Y4.1MC1 pending, Y5.1MC23 in finshing, metagenome done (draft)    
Burkholderia cenocepacia AU 1054 Finished 6/7/06 7.30 Mb
Burkholderia cenocepacia HI2424 Finished 11/6/06 7.70 Mb
Chromohalobacter salexigens DSM 3043 Finished 4/19/06 3.90 Mb
Clostridium beijerincki NCIMB 8052 Finished 6/27/07 7.80 Mb
Clostridium phytofermentans ISDg Finished 11/26/2007 5 Mb
Deinococcus geothermalis DSM 11300 Finished 10/17/2007 3 Mb
Frankia sp. CcI3 Finished 1/14/05 (draft) 5.43 Mb
Frankia sp. EAN1pec Finished 10/17/2007 10 Mb
Jannaschia sp. CCS1 Finished 3/1/06 4.5 Mb
Nocardioides sp. JS614 Finished 1/3/07 5.5 Mb
Paracoccus denitrificans PD1222 Finished 1/3/07 3.70 Mb
Polaromonas sp. JS666 Finished 4/12/06 5.20 Mb
Prochlorococcus marinus NATL2A Finished 4/11/05 2 Mb
Psychrobacter cryohalolentis K5 Finished 4/19/06 3.20 Mb
Silicibacter sp. TM1040 Finished 6/7/06 3.20 Mb
Solibacter usitatus Ellin6076 Finished 10/30/06 10.20 Mb
Sphingopyxis alaskensis RB2256 Finished 6/7/06 3.20 Mb
Sulfurimonas denitrificans DSM 1251 Finished 2/27/05 2.20 Mb
Synechococcus sp. CC9605 (oligotrophic) Finished 2/26/05 2.5 Mb
Synechococcus sp. CC9902 (coastal) Finished 2/26/05 2.5 Mb
Thermoanaerobacter pseudethanolicus 39E Finished 2/13/08 3 Mb
Thermoanaerobacter sp. X514 Finished 2/13/08 3 Mb
Thermus aquaticus Y51MC23 In finishing    
Thiobacillus denitrificans ATCC 25259 Finished 10/6/04 3 Mb
Thiomicrospira crunogena XCL-2 Finished 5/13/05 2.40 Mb

Eukaryotes

Organism Status* Public Release** Genome Size
Glomus intraradices In production   15 Mb
Laccaria bicolor In finishing (at Stanford) Released 40 Mb
Pichia stipitis, CBS 6054 Finished Released 12 Mb

Communities

Organism Status* Public Release** Genome Size
200 BACs from anaerobic bioreactor granules Finished   ~100 Mb
acid mine drainage community Done (draft)   ~80 Mb
Picoplankton BACS from HOTS site In production   ~150 Mb
Boiling thermal pool In production   ~50 Mb

*"Pending" indicates that we are waiting for DNA or the DNA is waiting to enter the production process; "in production" includes both library creation and production sequencing; "draft assembly" is the first assembly, made without finishing the genome; "finishing" is postproduction work not carried out for all organisms; "final assembly" is the process of assembling the finished genome; genomes on which we do not plan further work are labeled "done".

**"Reads released" indicates that reads have been sent to the GenBank Trace Archive; release dates indicate the date an assembly was made publicly available.