Bacterial pseudogenes and within-species heterogeneity

Subterminal nighttime Jon Eisen posted around a new material by Chih-Horng Kuo and Queen Ochman, near the evolutionary divinity of bacterial pseudogenes (PLoS Biology: The Quenching Mechanics of Bacterial Pseudogenes).  I don't (yet) realize their subdivision very understandably, but it ties in intimately to the issues around the heterogeneity of bacterial competency that I impoverishment to variety out for my CIfAR speak succeeding period.

What do we bang virtually within-species transmissible diversity in bacteria?  The big proceeds is ngo genome and ancillary genome.

In most (all?) species, distinguishable strains change a core set of genes in vulgar; usually these egest up around 80% of apiece exertion's cistron set (emblematic extent ~70%-90%).  These core genes are usually syntenic.  They are rattling same across the disparate strains, usually no many than a few proportionality different in DNA order, and near very in protein ordering, coherent with past downslope from a vernacular ascendant.  These shared-by-descent genes are what justifies grouping the strains as representatives of a only 'species'.

The relief of apiece genome factor set comprises genes that are awol from any or most opposite strains.  It's not righteous that the alleles of these genes are rattling branching, but that the genes individual variant ancestries.  Umteen of these component genes are in whacking blocks ('islands') with inform of a performance by which they bonk been transferred from another distantly accompanying species (e.g. phage, integron or dna sequences, flanking tRNA genes).  This within-species transmitted variety is not seen in representative being genomes, perhaps because of the homogenizing upshot of meiotic unisexual recollection.

Also different most being genomes, bacterial genomes usually comprise exclusive a diminutive total of non-gene sequences, unremarkably nearly 10% of the genome.  This is near exclusively intergenic; introns are very thin and usually take other genes (excisionases and militarization genes).