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Cross-species gene-family fluctuations reveal the dynamics of horizontal transfers.

TitleCross-species gene-family fluctuations reveal the dynamics of horizontal transfers.
Publication TypeJournal Article
Year of Publication2014
AuthorsGrilli, J, Romano, M, Bassetti, F, Cosentino Lagomarsino, M
JournalNucleic Acids Res
Volume42
Issue11
Pagination6850-60
Date Published2014
ISSN1362-4962
KeywordsEvolution, Molecular, Gene Duplication, Gene Transfer, Horizontal, Models, Genetic, Multigene Family
Abstract

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.

DOI10.1093/nar/gku378
Alternate JournalNucleic Acids Res.
PubMed ID24829449
PubMed Central IDPMC4066789