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 5265. Genome Announcements 2(3). pii: e00470-14. doi: 10.1128/genomeA.00470-14.
• Dictyoglomus thermophilum H-6-12 genome
  • Coil DA, Badger JH, Forberger HC, Riggs F, Madupu R, Fedorova N, Ward N, Robb FT, Eisen JA. 2014. Complete Genome Sequence of the Extreme Thermophile Dictyoglomus thermophilum H-6-12. Genome Announc. 2(1). pii: e00109-14. doi: 10.1128/genomeA.00109-14. PMID: 24558247.
• Chrysiogenes arsenatis DSM11915
  • Coil DA, Lo JR, Chen R, Ward N, Robb FT, Eisen JA. 2013. Draft Genome Sequence of the arsenate respiring bacterium Chrysiogenes arsenatis DSM11915. Genome Announcements 1(6): e00953-13. doi:10.1128/genomeA.00953-13.
• 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:

• STAP
  • Wu D, Hartman A, Ward N, Eisen JA. 2008. An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP). PLoS ONE 3(7): e2566. PMID: 18596968. PDF.
  • STAP Software page.
  • Blog post by Mike the Mad Biologist.
  • Blogged about by Genome Technology and Jonathan Eisen and Bora

• AMPHORA
  • Wu M, Eisen JA. 2008. A simple, fast, and accurate method of phylogenomic inference. Genome Biology 9(1): R151. PMID: 18851752. PDF.
  • AMPHORA software page
  • Faculty of 1000 reviews
  • Blogged about by Larry Moran

• APIS

Other papers supported by this grant are listed below

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

• Nature News article “The challenge of microbial diversity: Out on a limb.“
• Carl Zimmer Discover article “Glimpses of a fourth domain.“
• Carl Zimmer Discover article #2 “Trouble in the fourth domain.“
• Newsy video post
• Economist Story 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.

• Commentary

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