Quantifying evolutionary dynamics of the basic genome of E. coli

TL;DR

This study quantifies the evolutionary dynamics of E. coli's basic genome, revealing that horizontal transfer of large genomic segments significantly drives divergence and adaptation, primarily mediated by phages through generalized transduction.

Contribution

It provides a detailed analysis of horizontal transfer events and their impact on E. coli genome evolution, highlighting the role of phages in mediating large segment transfers.

Findings

Horizontal transfer of large segments is the main divergence driver.

HT events contribute 12 times more SNPs than point mutations.

Most strain pairs share little to no genome material with their ancestor.

Abstract

The ~4-Mbp basic genome shared by 32 independent isolates of E. coli representing considerable population diversity has been approximated by whole-genome multiple-alignment and computational filtering designed to remove mobile elements and highly variable regions. Single nucleotide polymorphisms (SNPs) in the 496 basic-genome pairs are identified and clonally inherited stretches are distinguished from those acquired by horizontal transfer (HT) by sharp discontinuities in SNP density. The six least diverged genome-pairs each have only one or two HT stretches, each occupying 42-115-kbp of basic genome and containing at least one gene cluster known to confer selective advantage. At higher divergences, the typical mosaic pattern of interspersed clonal and HT stretches across the entire basic genome are observed, including likely fragmented integrations across a restriction barrier. A simple model suggests that individual HT events are of the order of 10-kbp and are the chief contributor to genome divergence, bringing in almost 12 times more SNPs than point mutations. As a result of continuing horizontal transfer of such large segments, 400 out of the 496 strain-pairs beyond genomic divergence of share virtually no genomic material with their common ancestor. We conclude that the active and continuing horizontal transfer of moderately large genomic fragments is likely to be mediated primarily by a co evolving population of phages that distribute random genome fragments throughout the population by generalized transduction, allowing efficient adaptation to environmental changes.