The fraction of horizontally transferred genes in Methanosarcina

The fraction of horizontally transferred genes in Methanosarcina spp. decreases with time well, in some sense date of HGT: Methnosarcinal es, Methanosarcina ceae, Methanosarcina,

Bacterial species • • Morphology of cells and colonies Catabolism (metabolic abilities) Anabolism (auxotrophy) Cell wall components • ≥ 70% by DNA-DNA hybridization, ≤ 5ºC ∆Tm (Wayne et al. , 1987) – 'gold standard'. • ≥ 97% 16 S r. RNA sequence similarity (Stackebrandt and Goebel, 1994)

Gene complements (gene-ome) • text

Pan-genomes • Total set of genes in all strains of a species / genus (Tettelin et al, , 2005): – core ((universal genome): present in (almost) all strains – periphery: present in some strains – unique: (almost) strain-specific

Escherichia + Shigella. Gene occurrence in strains

Sum of three exponents (Wolf&Koonin) y = exp (– 0. 53 x + 8. 30) + exp (– 0. 02 x + 4. 41) + exp (0. 60 x – 12. 27)

Sum of two power laws y = 4400·x– 1. 72 + 674· (32–x)– 1. 26

Add Salmonella – get internal peaks Universal genome of Salmonella Universal genome of Escherichia

Core genome (still shrinks) EC+Shi filtered EC+Shi unfiltered EC+Shi+Sal filtered

Pan-genome is not saturated EC+Shi+Sal unfiltered EC+Shi+Sal unfiltered

Pan-genome increase per added genome EC+Shi unfiltered EC+Shi+Sal unfiltered EC+Shi+Sal filtered

Fractional pan-genome stabilizes number of genes sawtooth pattern due to rounding effects number of genomes fraction of genomes

Double pan-genome (Escherichia vs Salmonella):

Double pan-genome (Escherichia vs Shigella): No Escherichiaspecific periphery

Double pan-genome (pathogen vs commensal Escherichia):

R. Lan, P. R. Reeves / Microbes and Infection 4 (2002) 1125 -113

Escherichia-Salmonella division in trees 44% ordered trees 74% ordered trees 88 % ordered trees

Escherichia-Salmonella division in trees, groups w/o paralogs 55% ordered trees 81% ordered trees 92 % ordered trees