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Shotgun DNA Sequencing

When the Human Genome Mapping Project began in earnest, the allocation of large funding and the opening of dedicated research facilities promised much for the rapid improvement of DNA sequencing methods and, as a consequence, sequencing rates and throughput. Today, several years later, so ...

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Persistence Mechanisms of Conjugative Plasmids

Are plasmids selfish parasitic DNA molecules or an integrated part of the bacterial genome? This chapter reviews the current understanding of the persistence mechanisms of conjugative plasmids harbored by bacterial cells and populations. The diversity and intricacy of mechanis ...

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The Integron/Gene Cassette System: An Active Player in Bacterial Adaptation

The integron includes a site-specific recombination system capable of integrating and expressing genes contained in structures called mobile gene cassettes. Integrons were originally identified on mobile elements from pathogenic bacteria and were found to be a major reservoir ...

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Ancient Gene Transfer as a Tool in Phylogenetic Reconstruction

Although horizontal gene transfer (HGT) is often considered as a disruptive force in reconstructing organismal phylogeny, it can also be a valuable phylogenetic tool. A gene in the net of life is often horizontally transferred to the ancestor of a major lineage. If the gene is retained in the recipi ...

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The Tree of Life Viewed Through the Contents of Genomes

A universal Tree of Life has been a longstanding goal of the biosciences. The most common Tree of Life, based on the small subunit rRNA gene, may or may not represent the phylogenetic history of microorganisms. The horizontal transfer of genes from one taxon to another provides a means by which each gene may ...

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Horizontal Gene Transfer and the Evolution of Methanogenic Pathways

Horizontal gene transfer (HGT) is a driving force in the evolution of metabolic pathways, allowing novel enzymatic functions that provide a selective advantage to be rapidly incorporated into an organism’s physiology. Here, the role of two HGT events in the evolution of methanogenesis is d ...

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Composition-Based Methods to Identify Horizontal Gene Transfer

The detection of horizontal gene transfer (HGT) events has become an increasingly important issue in recent years. Here we discuss a simple theoretical analysis based on the in silico artificial addition of known foreign genes from different prokaryotic groups into the genome of Escheri ...

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Detection and Quantitative Assessment of Horizontal Gene Transfer

This chapter discusses the pros and cons of the existing computational methods for the detection of horizontal (or lateral) gene transfer and highlights the genome-wide studies utilizing these methods. The impact of horizontal gene transfer (HGT) on prokaryote genome evolution is dis ...

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Testing Phylogenetic Methods to Identify Horizontal Gene Transfer

The subject of this chapter is to describe the methodology for assessing the power of phylogenetic HGT detection methods. Detection power is defined in the framework of hypothesis testing. Rates of false positives and false negatives can be estimated by testing HGT detection methods on HGT- ...

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Untangling Hybrid Phylogenetic Signals: Horizontal Gene Transfer and Artifacts of Phylogenetic Reconstruction

Phylogenomic methods can be used to investigate the tangled evolutionary relationships among genomes. Building ‘all the trees of all the genes’ can potentially identify common pathways of horizontal gene transfer (HGT) among taxa at varying levels of phylogenetic depth. Phylogene ...

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Experimental Evolution of an Essential Bacillus Gene in an E. coli Host

The acquisition of foreign genes by HGT potentially greatly speeds up adaptation by allowing faster evolution of beneficial traits. The evolutionary integration of novel genes into host gene expression and physiology is critical for adaptation by HGT, but remains largely unknown. We a ...

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Construction and Use of Flow Cytometry Optimized Plasmid-Sensor Strains

Determining the stability of plasmids in bacterial populations is traditionally performed by isolating a large number of clones followed by screening for the presence of plasmids by replica transfer to plasmid-selective agar plates. This is often a laborious task, especially when the ...

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Mass Action Models Describing Extant Horizontal Transfer of Plasmids: Inferences and Parameter Sensitivities

Predicting the fate of horizontally transmissible elements in extant microbial communities might be facilitated by the availability of suitable mathematical models. Since the mid-1970s, mass action models have been introduced to describe the transfer of conjugal and mobiliza ...

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Interdomain Transfers of Sugar Transporters Overcome Barriers to Gene Expression

Horizontal gene transfer (HGT) is nature’s mechanism for sharing evolved physiological traits among the members of microbial communities. The extent to which such transfers can be successful is best illustrated by the fact that Archaea-derived genes are found in many bacterial genome ...

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The Role of Horizontal Gene Transfer in Photosynthesis, Oxygen Production, and Oxygen Tolerance

One of the pivotal events during the early evolution of life was the advent of oxygenic photosynthesis, responsible for producing essentially all of the free oxygen in Earth’s atmosphere. This molecular innovation required the development of two tandemly linked photosystems that gen ...

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Horizontal Gene Transfer in Cyanobacterial Signature Genes

Comparison of 15 phylogenetically diverse cyanobacterial genomes identified an updated list of 183 signature genes that are widely found in cyanobacteria but absent in non-cyanobacterial species. These signature genes comprise the unique portion of the core cyanobacterial ph ...

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Population Genomics and the Bacterial Species Concept

In recent years, the importance of horizontal gene transfer (HGT) in bacterial evolution has been elevated to such a degree that many bacteriologists now question the very existence of bacterial species. If gene transfer is as rampant as comparative genomic studies have suggested, how could ...

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A Critique of Prokaryotic Species Concepts

Developments in DNA sequencing and population genetics analyses have revealed unanticipated complexity in prokaryotic variation. The observation that genetic traits are horizontally inherited at unexpected rates within and between closely related asexually reprodu ...

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What Antimicrobial Resistance Has Taught Us About Horizontal Gene Transfer

Horizontal gene transfer (HGT) has been responsible for the dissemination of numerous antimicrobial-resistance determinants throughout diverse bacterial species. The rapid and broad dissemination of resistance determinants by HGT, and subsequent selection for resist ...

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Potential for Horizontal Gene Transfer in Microbial Communities of the Terrestrial Subsurface

The deep terrestrial subsurface is a vast, largely unexplored environment that is oligotrophic, highly heterogeneous, and may contain extremes of both physical and chemical factors. In spite of harsh conditions, subsurface studies at several widely distributed geographic sites ...

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