Cross-species gene-family fluctuations reveal the dynamics of horizontal transfers.
Prokaryotes vary their protein repertoire mainly through horizontal transfer and gene loss. To elucidate the links between these processes and the cross-species gene-family statistics, we perform a large-scale data analysis of the cross-species variability of gene-family abundance (the number of members of the family found on a given genome). We find that abundance fluctuations are related to the rate of horizontal transfers. This is rationalized by a minimal theoretical model, which predicts this link. The families that are not captured by the model show abundance profiles that are markedly peaked around a mean value, possibly because of specific abundance selection. Based on these results, we define an abundance variability index that captures a family's evolutionary behavior (and thus some of its relevant functional properties) purely based on its cross-species abundance fluctuations. Analysis and model, combined, show a quantitative link between cross-species family abundance statistics and horizontal transfer dynamics, which can be used to analyze genome 'flux'. Groups of families with different values of the abundance variability index correspond to genome sub-parts having different plasticity in terms of the level of horizontal exchange allowed by natural selection.
Dipartimento di Fisica e Astronomia "G. Galilei", Università di Padova, Via Marzolo 8, I-35131 Padova, Italy.
Jacopo
J
Grilli
Dipartimento di Fisica, Università degli Studi di Milano, via Celoria, 16, 20133 Milano, Italy.
Mariacristina
M
Romano
Università di Pavia, Dipartimento di Matematica, via Ferrata 1, 27100 Pavia, Italy.
Federico
F
Bassetti
CNRS, UMR 7238, Paris, France Sorbonne Universités, UPMC Université Paris 06, UMR 7238 Computational and Quantitative Biology, Genomic Physics Group, 15 rue de l'École de Médecine, Paris, France marco.cosentino-lagomarsino@upmc.fr.
Marco
M
Cosentino Lagomarsino
D019143:Evolution, Molecular; D020440:Gene Duplication; D022761:Gene Transfer, Horizontal; D008957:Models, Genetic; D005810:Multigene Family