CREATED: 200904020303 LINK: url:~/Modules/Literature/Lerat2003.pdf TITLE: Multigene phylogeny using complete genomes of gamma-Proteobacteria gamma-Proteobacteria: model of bacteria diversification, includes free-living and communal species, intracellular symbionts, and plant and animal pathogens
LGT is known to be extensive in this group, most often involves uptake of genes assuming functions that are not represented in the recipient and arriving from distantly related bacteria or phage.
Replacement of single-copy orthologous genes is rare, most single-copy orthologous genes show broad phylogenetic agreement that reflects the organismal relationships
Construction of gene families: consider ratio of BLASTP score to maximal BLASTP score (self comparison). Distribution is bimodal, separation occurs at about 30%. Protein was included in a family if this criterion was satisfied for at least one member