aTOL Bacterial Phylogenomics

While at TIGR Jonathan Eisen received a grant from the National Science Foundation as part of their “Assembling the Tree of Life” program.  CoPIs on the grant were Naomi Ward at TIGR and Frank Robb at University of Maryland.

The goal of this project was to sequence and then use the genomes of representatives of eight phyla of bacteria for which, at the time, there were cultured species but not available genome sequences.

The organisms selected are listed below with links to genome papers, data, etc:

  • Thermomicrobium roseum DSM 159
    • Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham JE, Bryant DA, Robb FT Colman AS, Tallon LJ, Badger JH, Madupu R, Ward NL, Eisen JA. 2009. Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PLoS ONE 4(1): e4207. PMID: 19148287. PDF.
  • Coprothermobacter proteolyticus DSM 5265
    • Alexiev A, Coil DA, Badger JH, Enticknap J, Ward N, Robb FT, Eisen JA. 2014.Complete Genome Sequence of Coprothermobacter proteolyticus DSM 5265Genome Announcements 2(3). pii: e00470-14. doi: 10.1128/genomeA.00470-14.
  • Dictyoglomus thermophilum H-6-12 genome
  • Chrysiogenes arsenatis DSM11915
  • Synergistes jonesii
  • Thermodesulfobacterium commune DSM 2178
  • Thermodesulfovibrio yellowstonii DSM 11347

The project also had many goals in terms of informatics methods developments. Software development supported by the project included those listed below:

  • APIS

 

Other papers supported by this grant are listed below

Wu D, Wu M, Halpern A, Rusch D, Yooseph S, Frazier M, Venter JCEisen JA. 2011.Stalking the fourth domain in metagenomic data: searching for and possible discovery of novel deep branches in phylogenetic treesPLoS ONE 6(3): e18011. PMID: 21437252. PDF.

Eisen JA. 2005. Coordinating efforts to understand microbes in the environment.Letter to the Editor. Microbe, 71(4): 157.  PDF.

Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Paulsen IT, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson JD, Hoffman J, Parsons R, Baden-Tillson H, Pfannkock C, Rogers Y-H, and Smith HO. 2004. Environmental whole genome shotgun sequencing: the Sargasso Sea. Science 304: 66-74. PMID: 15001713. PDF.  Supplement.PDF.

Eisen JA, Fraser CM. 2003. Phylogenomics: intersection of evolution and genomics.Science 300: 1706-1707. PMID: 12805538. PDF.

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