ScienceDaily (May 18, 2010) — A new "tree of life" has been constructed by researchers at the Virginia Bioinformatics Institute (VBI) at Virginia Tech for the gamma-proteobacteria, a large group of medically and scientifically important bacteria that includes Escherichia coli, Salmonella typhimurium, and other disease-causing organisms.
By building powerful phylogenetic trees, scientists are able to quickly identify similarities and differences between the make-up of many different organisms, crucial information in the search for treatments to fight anything from the bugs that cause food poisoning to the pathogens that cause life-threatening diseases such as cholera and the plague.
A "tree of life," or phylogenetic tree, is a way to visualize the evolutionary relationships among different biological species that have descended from a common ancestor. The gamma-proteobacteria tree developed by VBI researchers was reconstructed using powerful computers from as many as 30 million data points of bacterial sequence information.
Kelly Williams, Research Investigator at VBI, remarked: "Ribosomal RNA is one of the central components of the ribosome, the protein manufacturing machinery of all living cells. In the past, researchers have often depended on looking at a single ribosomal RNA gene to construct evolutionary relationships for their tree-building efforts. The method we use to make our tree of life uses hundreds of different genes and integrates much more information than can be gleaned from the traditional single gene approach. We firmly believe that the multi-gene or phylogenomics approach should become the standard for tree-building when several genome sequences are available, which is now the case for most bacterial groups."
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Journal of Bacteriology, May 2010, p. 2305-2314, Vol. 192, No. 9
0021-9193/10/$12.00+0 doi:10.1128/JB.01480-09
Copyright © 2010, American Society for Microbiology. All Rights Reserved.
Phylogeny of Gammaproteobacteria ,
Journal of Bacteriology, May 2010, p. 2305-2314, Vol. 192, No. 9
0021-9193/10/$12.00+0 doi:10.1128/JB.01480-09
Copyright © 2010, American Society for Microbiology. All Rights Reserved.
Phylogeny of Gammaproteobacteria ,
Kelly P. Williams,* Joseph J. Gillespie, Bruno W. S. Sobral, Eric K. Nordberg, Eric E. Snyder, Joshua M. Shallom, and Allan W. Dickerman
Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24061
Received 11 November 2009/ Accepted 4 February 2010
The phylogeny of the large bacterial class Gammaproteobacteria has been difficult to resolve. Here we apply a telescoping multiprotein approach to the problem for 104 diverse gammaproteobacterial genomes, based on a set of 356 protein families for the whole class and even larger sets for each of four cohesive subregions of the tree. Although the deepest divergences were resistant to full resolution, some surprising patterns were strongly supported. A representative of the Acidithiobacillales routinely appeared among the outgroup members, suggesting that in conflict with rRNA-based phylogenies this order does not belong to Gammaproteobacteria; instead, it (and, independently, "Mariprofundus") diverged after the establishment of theAlphaproteobacteria yet before the betaproteobacteria/gammaproteobacteria split. None of the orders Alteromonadales, Pseudomonadales, or Oceanospirillales weremonophyletic; we obtained strong support for clades that contain some but exclude other members of all three orders. Extreme amino acid bias in the highly A+T-rich genome of Candidatus Carsonella prevented its reliable placement withinGammaproteobacteria, and high bias caused artifacts that limited the resolution ofthe relationships of other insect endosymbionts, which appear to have had multiple origins, although the unbiased genome of the endosymbiont Sodalis acted as an attractor for them. Instability was observed for the root of the Enterobacteriales, with nearly equal subsets of the protein families favoring one or the other of two alternative root positions; the nematode symbiont Photorhabdus was identified as a disruptor whose omission helped stabilize the Enterobacteriales root.
* Corresponding author. Mailing address: Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061. Phone: (540) 231-7121. Fax: (540) 231-2606. E-mail: kellwill@vt.edu
Published ahead of print on 5 March 2010.
Supplemental material for this article may be found at http://jb.asm.org/.
Present address: Department of Fisheries and Wildlife Sciences, Integrated Life Sciences Building (0913), 1981 Kraft Drive, Blacksburg, VA 24061.
Journal of Bacteriology, May 2010, p. 2305-2314, Vol. 192, No. 9
0021-9193/10/$12.00+0 doi:10.1128/JB.01480-09
Copyright © 2010, American Society for Microbiology. All Rights Reserved.
Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24061
Received 11 November 2009/ Accepted 4 February 2010
The phylogeny of the large bacterial class Gammaproteobacteria has been difficult to resolve. Here we apply a telescoping multiprotein approach to the problem for 104 diverse gammaproteobacterial genomes, based on a set of 356 protein families for the whole class and even larger sets for each of four cohesive subregions of the tree. Although the deepest divergences were resistant to full resolution, some surprising patterns were strongly supported. A representative of the Acidithiobacillales routinely appeared among the outgroup members, suggesting that in conflict with rRNA-based phylogenies this order does not belong to Gammaproteobacteria; instead, it (and, independently, "Mariprofundus") diverged after the establishment of theAlphaproteobacteria yet before the betaproteobacteria/gammaproteobacteria split. None of the orders Alteromonadales, Pseudomonadales, or Oceanospirillales weremonophyletic; we obtained strong support for clades that contain some but exclude other members of all three orders. Extreme amino acid bias in the highly A+T-rich genome of Candidatus Carsonella prevented its reliable placement withinGammaproteobacteria, and high bias caused artifacts that limited the resolution ofthe relationships of other insect endosymbionts, which appear to have had multiple origins, although the unbiased genome of the endosymbiont Sodalis acted as an attractor for them. Instability was observed for the root of the Enterobacteriales, with nearly equal subsets of the protein families favoring one or the other of two alternative root positions; the nematode symbiont Photorhabdus was identified as a disruptor whose omission helped stabilize the Enterobacteriales root.
* Corresponding author. Mailing address: Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061. Phone: (540) 231-7121. Fax: (540) 231-2606. E-mail: kellwill@vt.edu
Published ahead of print on 5 March 2010.
Supplemental material for this article may be found at http://jb.asm.org/.
Present address: Department of Fisheries and Wildlife Sciences, Integrated Life Sciences Building (0913), 1981 Kraft Drive, Blacksburg, VA 24061.
Journal of Bacteriology, May 2010, p. 2305-2314, Vol. 192, No. 9
0021-9193/10/$12.00+0 doi:10.1128/JB.01480-09
Copyright © 2010, American Society for Microbiology. All Rights Reserved.
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0021-9193/07/$08.00+0 doi:10.1128/JB.00269-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.
A Robust Species Tree for the Alphaproteobacteria ,
Kelly P. Williams,* Bruno W. Sobral, and Allan W. Dickerman
Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061
Received 16 February 2007/ Accepted 24 April 2007
The branching order and coherence of the alphaproteobacterial orders have not been well established, and not all studies have agreed that mitochondria arose from within the Rickettsiales. A species tree for 72 alphaproteobacteria was produced from a concatenation of alignments for 104 well-behaved protein families. Coherence was upheld for four of the five orders with current standing that were represented here by more than one species. However, the family Hyphomonadaceae was split from the other Rhodobacterales, forming an expanded group with Caulobacterales that also included Parvularcula. The three earliest-branching alphaproteobacterial orders were the Rickettsiales, followed by the Rhodospirillales and then the Sphingomonadales. The principal uncertainty is whether the expanded Caulobacterales group is more closely associated with the Rhodobacterales or the Rhizobiales. The mitochondrial branch was placed within the Rickettsiales as a sister to the combined Anaplasmataceae andRickettsiaceae, all subtended by the Pelagibacter branch. Pelagibacter genes will serve as useful additions to the bacterial outgroup in future evolutionary studies of mitochondrial genes, including those that have transferred to the eukaryotic nucleus.
* Corresponding author. Mailing address: Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061. Phone: (540) 231-7121. Fax: (540) 231-2606. E-mail: kellwill@vt.edu
Published ahead of print on 4 May 2007.
Supplemental material for this article may be found at http://jb.asm.org/.
Journal of Bacteriology, July 2007, p. 4578-4586, Vol. 189, No. 13
0021-9193/07/$08.00+0 doi:10.1128/JB.00269-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.
Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061
Received 16 February 2007/ Accepted 24 April 2007
The branching order and coherence of the alphaproteobacterial orders have not been well established, and not all studies have agreed that mitochondria arose from within the Rickettsiales. A species tree for 72 alphaproteobacteria was produced from a concatenation of alignments for 104 well-behaved protein families. Coherence was upheld for four of the five orders with current standing that were represented here by more than one species. However, the family Hyphomonadaceae was split from the other Rhodobacterales, forming an expanded group with Caulobacterales that also included Parvularcula. The three earliest-branching alphaproteobacterial orders were the Rickettsiales, followed by the Rhodospirillales and then the Sphingomonadales. The principal uncertainty is whether the expanded Caulobacterales group is more closely associated with the Rhodobacterales or the Rhizobiales. The mitochondrial branch was placed within the Rickettsiales as a sister to the combined Anaplasmataceae andRickettsiaceae, all subtended by the Pelagibacter branch. Pelagibacter genes will serve as useful additions to the bacterial outgroup in future evolutionary studies of mitochondrial genes, including those that have transferred to the eukaryotic nucleus.
* Corresponding author. Mailing address: Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061. Phone: (540) 231-7121. Fax: (540) 231-2606. E-mail: kellwill@vt.edu
Published ahead of print on 4 May 2007.
Supplemental material for this article may be found at http://jb.asm.org/.
Journal of Bacteriology, July 2007, p. 4578-4586, Vol. 189, No. 13
0021-9193/07/$08.00+0 doi:10.1128/JB.00269-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.
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