from Luo et al (2011) in Microbial Population Genetics

Generally, microorganisms, in particular prokaryotes often lack morphological and behavioral characters amenable to phylogenetic analysis. Such a lack of information in these areas makes gene sequence information the most prevalent source of data for phylogenetic analysis in pre-genomic era. Molecular phylogenetics based on single genes, in particular the small-subunit rRNA (SSU rRNA) , has laid the foundation for a modern classification system, conceptually represented by the 'universal tree of life'. However, phylogenetic trees based on single genes or gene families may show conflict results due to a variety of problem, such as mutational saturation of the single genes and horizontal gene transfer. Consequently, although SSU rRNA gene sequence continue to be considered as molecular criteria for species delineation, it is anticipated that much additional taxonomic information can be extracted from complete genome sequences.

Now that large-scale genome-sequencing projects are sampling many organismal lineages, it is becoming possible to compare large data sets of DNA or protein sequences to study speciation and evolution. The steady increase in the number of completely sequenced prokaryotic genomes has created a boom for bioinformatics. With more than 700 prokaryotic genomes completely sequenced, there has been an increasing interest in the use of various characters in whole genomes for prokaryotic genomes studies. This is giving birth to a brand new field of research - phylogenomics. Phylogenomics use entire genomes to infer a species tree and has become the de facto standard for reconstructing reliable phylogenies.

One major branch of phylogenomics involves the use of these data to reconstruct the evolutionary history of organisms. Access to large amount of genomic data could potentially alleviate problems associated with single-gene based phylogenetics. This is because a large number of characters can now be used for phylogenetic analysis to avoid biases. With this increase, the emphasis of phylogenetic inference is shifting from the search for informative characters to the development of better reconstruction methods using genomic data. Existing models used in tree-building algorithms only partially take into account molecular evolutionary processes, and phylogenomic inference will benefit from an increased understanding of these mechanisms. Interestingly, phylogenomics is also providing the opportunity to use new 'morphological-like' characters that are based on genome structure, such as rare genomic changes (RGCs). The integration of genomics data into the phylogenetics is still at an early stage. Given the breadth of organismal diversity, the gene-scale era of phylogenetics is still an invaluable asset to the pursuit of the Tree of Life. Comparative genomics, with its ability and potential to vastly increase both the amount and type of molecular data available for a small but critical fraction of biodiversity, is bound to play an increasingly important role in efforts to assemble a robust picture of the Tree of Life.

BPhyOG A database for overlapping genes in prokaryotic genomes
BPhyOG (Bacterial Phylogeny based on Overlapping Genes) is an online interactive server for reconstructing completely sequenced bacterial genomes on the basis of their shared overlapping genes. It provides two tree-reconstruction methods: Neighbor Joining (NJ) and Unweighted Pair-Group Method using Arithmetic averages (UPGMA). Users can apply the desired method to generate phylogenetic trees, which are based on an evolutionary distance matrix for the selected genomes. The distance between two genomes is defined by the normalized number of their shared OG pairs. BPhyOG also allows users to browse the OGs that were used to infer the phylogenetic relationships. It provides detailed annotation for each OG pair and the features of the component genes through hyperlinks. Users can also retrieve each of the homologous OG pairs that have been determined among 177 genomes. BPhyOG is useful tool for analyzing the tree of life and overlapping genes from a genomic standpoint. It currently includes 177 completely sequenced bacterial genomes containing 79,855 OG pairs, with their annotation and homologous OG pairs comprehensively integrated. The reliability of phylogenies and completeness of annotations make BPhyOG a comprehensive and powerful web server for genomic and genetic studies.

Tags: Microbial Population Genetics | Population Genetics | Analytic Tools in Comparative Genomics | Comparative Genomics | Comparative Genomics Tools | Comparative Microbial Genomics | Population Genetic Patterns and Evolutionary Implications | Microbial genomics