BLACKSBURG, Va., July 9, 2007 – A recently published paper from the Virginia Bioinformatics Institute (VBI) has been selected for inclusion in an online research service that highlights papers published in the biological sciences. Publications included in Faculty of 1000 Biology are recommended by some of the world’s leading researchers.

"A Robust Species Tree for the Alphaproteobacteria," which was authored by VBI Research Investigator Kelly Williams, VBI Executive and Scientific Director and Professor Bruno Sobral, and VBI Assistant Professor Allan Dickerman, was published in the July 2007 edition of the Journal of Bacteriology.1 In addition, the paper has been selected for Faculty of 1000 Biology-an online service consisting of a virtual "faculty" who highlight and evaluate the most interesting papers they read each month. Faculty of 1000 Biology reviewer Frank Robb, who serves as a professor and associate director of the Center of Marine Biology at the University of Maryland, recently selected the paper for evaluation.

"This is a groundbreaking study that demonstrates how the burgeoning genomic DNA sequence databases can provide ‘ground truth' confirmation and improvement of phylogenies based on rDNA sequences," Robb said in his review of the paper. "The additional consideration of 104 ‘well-behaved protein families' alongside the 16S- and 23S-rDNA based phylogeny of the Alphaproteobacteria provides a consensus branching order for this diverse group of Proteobacteria."

Faculty of 1000 Biology (www.f1000biology.com) was launched in 2002 and is composed of over 2,300 faculty members invited to comment on the most interesting papers they read each month from any source.

The full comments from Frank Robb, Professor and Associate Director of the Center of Marine Biology at the University of Maryland, are shown below.

1. Williams KP, Sobral BW, Dickerman AW (2007) A Robust Species Tree for the Alphaproteobacteria. J. Bacteriol. 189:4578-4586.

Full comments of Frank Robb, professor and associate director of the Center of Marine Biology at the University of Maryland, on the paper "A Robust Species Tree for the Alphaproteobacteria" (Williams KP, Sobral BW, Dickerman AW, 2007, J. Bacteriol. 189: 4578-4586).

This is a groundbreaking study that demonstrates how the burgeoning genomic DNA sequence databases can provide ‘ground truth' confirmation and improvement of phylogenies based on rDNA sequences. The additional consideration of 104 ‘well-behaved protein families' alongside the 16S- and 23S-rDNA based phylogeny of the Alphaproteobacteria provides a consensus branching order for this diverse group of Proteobacteria. The broader significance of the confirmed topology is that the position of the mitochondrial branch is now convincingly placed within the Rickettsiales, with the Pelagibacter group as a useful outgroup. The study elegantly resolves the disagreement between the 16S rDNA and 23S rDNA trees with extremely high bootstrap support values. This has particular significance since the Pelagibacter cluster includes the SAR11 organisms, which are abundant marine planktonic species. Taxonomic assignment of Pelagibacter-related genes within the burgeoning metagenomic database of oceanic bacteria will now be placed on a firm footing.

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Published by Susan Bland, July 09, 2007