Genomes in turmoil: Quantification of genome dynamics in prokaryote supergenomes

David M Kristensen,Alexander E Lobkovsky,Pere Puigbò,Yuri I Wolf,Eugene V Koonin

doi:10.1186/preaccept-1328480924130239

Abstract

Genomes in turmoil: Quantification of genome dynamics in prokaryote supergenomes

Highlights

IntroductionGenomes of bacteria and archaea (collectively, prokaryotes) appear to exist in incessant flux, expanding via horizontal gene transfer and gene duplication, and contracting via gene loss
Genomes of bacteria and archaea appear to exist in incessant flux, expanding via horizontal gene transfer and gene duplication, and contracting via gene loss
These patterns were mapped onto the phylogenetic tree of the respective alignable tight genome cluster (ATGC) and employed for the evolutionary reconstruction using Count, an maximum likelihood (ML) method based on a phylogenetic gene birth-and-death model [22]

Summary

Introduction

Genomes of bacteria and archaea (collectively, prokaryotes) appear to exist in incessant flux, expanding via horizontal gene transfer and gene duplication, and contracting via gene loss. Beyond the comparative genomic observations, estimates of the genome dynamics rates in prokaryotes have been obtained via explicit evolutionary reconstruction using maximum parsimony or maximum likelihood (ML) methods. These approaches typically employ the pattern of gene presence/absence in a set of species, which is mapped onto a guide phylogenetic tree [19,20,21,22,23]. Gene loss has been reported to be a more uniform, ‘clock-like’ process than gene gain, which shows a stronger episodic character [19,29] Taken together, these findings have inspired the concept of genome reduction as the ‘default’ evolutionary process counterbalanced by episodes of gene gain, primarily via HGT [34]

Methods

Results

Discussion

Conclusion