Title: Recombinant transfer in the basic genome of Escherichia coli

Abstract

An approximation to the ~4-Mbp basic genome shared by 32 strains of E. coli representing six evolutionary groups has been derived and analyzed computationally. A multiple-alignment of the 32 complete genome sequences was filtered to remove mobile elements and identify the most reliable ~90% of the aligned length of each of the resulting 496 basic-genome pairs. Patterns of single bp mutations (SNPs) in aligned pairs distinguish clonally inherited regions from regions where either genome has acquired DNA fragments from diverged genomes by homologous recombination since their last common ancestor. Such recombinant transfer is pervasive across the basic genome, mostly between genomes in the same evolutionary group, and generates many unique mosaic patterns. The six least-diverged genome-pairs have one or two recombinant transfers of length ~40–115 kbp (and few if any other transfers), each containing one or more gene clusters known to confer strong selective advantage in some environments. Moderately diverged genome pairs (0.4–1% SNPs) show mosaic patterns of interspersed clonal and recombinant regions of varying lengths throughout the basic genome, whereas more highly diverged pairs within an evolutionary group or pairs between evolutionary groups having >1.3% SNPs have few clonal matches longer than a few kbp. Many recombinant transfers appearmore » to incorporate fragments of the entering DNA produced by restriction systems of the recipient cell. A simple computational model can closely fit the data. As a result, most recombinant transfers seem likely to be due to generalized transduction by co-evolving populations of phages, which could efficiently distribute variability throughout bacterial genomes.« less

Authors:

Dixit, Purushottam D. ^[1]; Pang, Tin Yau ^[1]; Studier, F. William ^[1]; Maslov, Sergei ^[1]

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+ Show Author Affiliations

1. Biological, Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY 11973

Publication Date:

Tue Jul 07 00:00:00 EDT 2015

Research Org.:

Brookhaven National Laboratory (BNL), Upton, NY (United States)

Sponsoring Org.:

USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:

1235129

Alternate Identifier(s):

OSTI ID: 1214531

Report Number(s):

BNL-108341-2015-JA
Journal ID: ISSN 0027-8424

Grant/Contract Number:  

PM-031; ELS165; Internal research funding; SC00112704

Resource Type:

Journal Article: Published Article

Journal Name:

Proceedings of the National Academy of Sciences of the United States of America

Additional Journal Information:

Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Volume: 112 Journal Issue: 29; Journal ID: ISSN 0027-8424

Publisher:

Proceedings of the National Academy of Sciences

Country of Publication:

United States

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES; E. coli evolution; basic genome; core genome; recombinant transfer; generalized transduction