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Comparative genomics: the bacterial pan-genome
Current Opinion in Microbiology, 2008Bacterial genome sequencing has become so easy and accessible that the genomes of multiple strains of more and more individual species have been and will be generated. These data sets provide for in depth analysis of intra-species diversity from various aspects.
Tettelin H, Riley D, Cattuto C, Medini D
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The Organization of the Bacterial Genome
Annual Review of Genetics, 2008Many bacterial cellular processes interact intimately with the chromosome. Such interplay is the major driving force of genome structure or organization. Interactions take place at different scales—local for gene expression, global for replication—and lead to the differentiation of the chromosome into organizational units such as operons, replichores ...
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Bacterial Genome Reengineering
2011The web application PrimerPair at ecogene.org generates large sets of paired DNA sequences surrounding- all protein and RNA genes of Escherichia coli K-12. Many DNA fragments, which these primers amplify, can be used to implement a genome reengineering strategy using complementary in vitro cloning and in vivo recombineering. The integration of a primer
Jindan Zhou, Kenneth E. Rudd
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Phylogenetics and the Cohesion of Bacterial Genomes
Science, 2003Gene acquisition is an ongoing process in many bacterial genomes, contributing to adaptation and ecological diversification. Lateral gene transfer is considered the primary explanation for discordance among gene phylogenies and as an obstacle to reconstructing the tree of life.
Daubin, Vincent, Moran, N.A., Ochman, H.
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2012
Annotation of prokaryotic sequences can be separated into structural and functional annotation. Structural annotation is dependent on algorithmic interrogation of experimental evidence to discover the physical characteristics of a gene. This is done in an effort to construct accurate gene models, so understanding function or evolution of genes among ...
Tracey Allen K. Freitas +3 more
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Annotation of prokaryotic sequences can be separated into structural and functional annotation. Structural annotation is dependent on algorithmic interrogation of experimental evidence to discover the physical characteristics of a gene. This is done in an effort to construct accurate gene models, so understanding function or evolution of genes among ...
Tracey Allen K. Freitas +3 more
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Retrons, msDNA, and the bacterial genome
Cytogenetic and Genome Research, 2005Retrons are distinct DNA sequences that code for a reverse transcriptase (RT) similar to the RTs produced by retroviruses and other types of retroelements. Retron DNAs are commonly associated with prophage DNA and are found in the genomes of a wide variety of different bacteria. The retron RT is used to synthesize a strange satellite DNA known as msDNA.
Lampson, B. C., Inouye, M., Inouye, S.
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Bacteriophages and the Bacterial Genome [PDF]
, 2014 This chapter focuses on the doublestranded DNA (dsDNA) phages, and especially on the temperate phages. While virulent phages certainly perform transduction and engage in evolutionary sparring with their hosts and so influence their evolution, the chapter focuses mainly on the complex interactions of temperate phages with their hosts. Bacteriophages may
Roger W. Hendrix, Sherwood R. Casjens
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The Pyrosequencing Protocol for Bacterial Genomes
2015The pyrosequencing methodology was applied in 2005 by 454 Lifesciences to the emerging field of next generation sequencing (NGS), revolutionizing the way of DNA sequencing. In the last years the same strategy grew up and was technologically updated, reaching a high throughput in terms of amount of generated sequences (reads) per run and in terms of ...
Rizzi, Ermanno
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Microbe Magazine, 2008
One central microbiological question is what factors change the size and content of bacterial genomes. What causes such genomes to become smaller for microbes that live as intracellular parasites or as symbionts, and what novel functions do they incorporate and stably maintain? From comparative sequence analyses during the past decade, we know that the
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One central microbiological question is what factors change the size and content of bacterial genomes. What causes such genomes to become smaller for microbes that live as intracellular parasites or as symbionts, and what novel functions do they incorporate and stably maintain? From comparative sequence analyses during the past decade, we know that the
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2008
Since the mid-eighties, laboratories world-wide have endeavoured to determine the complete sequence of genomes from all kinds of living organisms. The first complete sequence of DNA bacteriophage ΦX174 appeared in 1978 (5386 nt (Sanger et al. 1978)), followed by that of bacteriophage lambda, using a shotgun technology, published in 1982 (48,502 bp ...
Claudine Médigue +2 more
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Since the mid-eighties, laboratories world-wide have endeavoured to determine the complete sequence of genomes from all kinds of living organisms. The first complete sequence of DNA bacteriophage ΦX174 appeared in 1978 (5386 nt (Sanger et al. 1978)), followed by that of bacteriophage lambda, using a shotgun technology, published in 1982 (48,502 bp ...
Claudine Médigue +2 more
openaire +2 more sources