Tree of Life -- What's New

The Tree of Life team will have three presentations at the 104th General Meeting of the American Society for Microbiology, in New Orleans, May 23-27: Jonathan Eisen will be presenting a seminar "Phylogenomics and the Axis of Evol", and a poster on our Tree of Life project.

Seminar: "Phylogenomics and the Axis of Evol"

Topic: R05 Comparative Genomics

Presenter:

J. A. Eisen1, N. Ward1, K. Penn1, K. E. Nelson1, E. M. O'Connor2, J. Enticknap2, F. T. Robb2
The Institute for Genomic Research, Rockville, MD
Center of Marine Biotechnology, Baltimore, MD.

Presentation Number: R-082

Poster Board Number: 409

Description:

The main goals of this project are

to increase the phylogenetic diversity of available complete bacterial genome sequences
to use those sequences to improve resolution of phylogenetic relationships within and among the bacterial phyla.

Based upon the current classification of bacteria and an excellent review paper (Hugenholtz, 2002), we selected eight bacterial phyla (Chrysiogenetes, Deferribacteres, Dictyoglomus, Nitrospira, Coprothermobacter, Synergistes, Thermodesulfobacteria, Thermomicrobium) for which there are cultured species but no genome sequences available. Our goal is to determine a complete genome sequence from a representative of each phylum; selection will be based on genome size, ease of cultivation, and relevance to the scientific community.

Prior to genome sequencing we will also sequence phylogenetic markers in addition to rRNA, to test the “phyla” status of these groups. We have commenced work on representatives of six phyla (Chrysiogenes arsenatis, Dictyoglomus thermophilum, Thermodesulfovibrio yellowstonii, Coprothermobacter proteolyticus, Thermodesulfobacterium commune, Thermomicrobium roseum). Genome size has been determined for T. roseum (2Mb with a 0.9Mb megaplasmid) and T. yellowstonii (2.4Mb), and shotgun DNA libraries have been constructed from D. thermophilum, T. yellowstonii, T. commune, and T. roseum.

Preliminary sequencing of these libraries yielded partial or complete sequences of additional phylogenetic markers (e.g., recA, rpoB, tufA, and HSP70). Analysis of these markers provides further evidence for the phylum status of Thermomicrobium (T. roseum), Nitrospira (T. yellowstonii) and Thermodesulfobacteria (T. commune). However, most alternative phylogenetic markers from D. thermophilum suggest it is not a true phylum of bacteria, rather a subgroup of the Firmicutes. We are also investigating the physiology of selected strains; with the exception of C. arsenatis, all are thermophiles, and all except T. roseum are strict anaerobes. New physiological data, including information on electron acceptors (nitrate, arsenate) used by C. arsenatis, will be presented.

Poster on APIS: an Automated Phylogenomic Inference System.

Topic: R07 Computational Analyses and Methods

Presenter:

J. H. Badger
The Institute for Genomic Research, Rockville, MD

Presentation Number: R-054

Poster Board Number: 379

Background:

The ever-growing number of available genomes has transformed the study of phylogenetics. Rather than simply inferring relationships between organisms on the basis of trees of commonly used phylogenetic markers (such as 16S rRNA), one can now compare trees of all genes from a genome for which homologs are available. In addition, not only can genomics help phylogenetics, but also vice-versa, as evolutionary relationships are a more reliable indicator of gene function than sequence similarity. However, a major drawback of analyzing a genome in this way is the excessive amount of manual effort required. I have attempted to reduce this manual effort by the creation of a web-based system (APIS) that automates the creation and interpretation of genomic phylogenetic analyses. Methods: APIS uses BLASTP or BLASTX to compare each predicted gene of a genome against a database of proteins from all completed genomes. The full-length sequences of each matching protein are extracted and aligned using CLUSTALW, and a neighbor-joining tree of each alignment is created by PAUP. The trees are automatically analyzed to identify the closest sequence and organism to the query leaf, and summaries over all genes being analyzed are generated. Results: APIS has proved to be a useful tool for the analysis of new genomes, and is in current use by several groups at TIGR. Conclusion: While useful in its existing form, APIS is being extended to handle alternative methods of phylogenetic analysis and additional forms of genomic analysis, such as codon bias.

Funded by NSF Tree of Life Program

Last Update:05/24/04