Words similar to genome-tree
Example sentences for: genome-tree
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In previous studies that employed similar approaches to genome-tree building, phylogenetically reasonable clades were observed after a simple omission of parasitic species [ 8 9 ] . Such an operation could be applied to the tree shown in Fig.
The most straightforward version of this type of analysis, to which we hereinafter refer to as 'genome-tree' building, involves scaling-up the traditional tree-building approach and analyzing the phylogenetic trees for multiple gene families (in principle, all families represented in many genomes), in an attempt to derive a consensus, 'organismal' phylogeny [ 3 4 5 ] . However, because of the wide spread of horizontal gene transfer and lineage-specific gene loss, at least in the prokaryotic world, comparison of trees for different families and consensus derivation may become highly problematic [ 6 7 ] . Probably due to all these problems, a pessimistic conclusion has been reached that prokaryotic phylogeny might not be reconstructable from protein sequences, at least with current phylogenetic methods [ 4 ] .
Here, we compare the topologies produced with five, largely independent approaches to genome-tree building: i) presence-absence of genomes in Clusters of Orthologous Groups of proteins (COGs); ii) conservation of local gene order (pairs of adjacent genes) among prokaryotic genomes; iii) distribution of percent identity between apparent orthologs; iv) sequence conservation in concatenated alignments of ribosomal proteins; v) comparative analysis of multiple trees reconstructed for representative protein families.
New criteria for genome-tree construction
Notably, in the quantitative comparison of tree topologies, the tree made of concatenated ribosomal protein alignments showed the closest similarity to the genome-tree based on the distributions of percent identity between orthologs (Table 2).
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