Special Issue "Bacterial Genomes and Their Evolution"

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Population and Evolutionary Genetics and Genomics".

Deadline for manuscript submissions: closed (30 November 2015)

Special Issue Editor

Guest Editor
Prof. Dr. J. Peter W. Young

Department of Biology, University of York, Heslington, York YO10 5DD, UK
Website | E-Mail
Fax: +44 1904 328505
Interests: bacterial genomes; population genetics; phylogenomics; phylogenetics; genome projects; genetic diversity

Special Issue Information

Dear Colleagues,

It is less than two decades since the first bacterial genome was sequenced, but now there are more than a thousand complete bacterial genome sequences available, with substantial but incomplete information on many more. Not only individual isolates, but uncultured organisms and whole bacterial communities can be sequenced. In recent years, the pace of data acquisition has quickened greatly with the development of higher-throughput sequencing. The completion of one more bacterial genome is no longer a major event, but the accumulation of information from such a large number of organisms provides many opportunities to explore general patterns and to identify special cases.

This Special Issue provides an Open Access forum to bring together a range of contributions to our understanding of bacterial genomes. These may include the presentation of new genomic data, comparative analyses based on published sequences, new insights and hypotheses, and reviews of relevant topics. We hope to provide an interesting cross-section of current work, and welcome significant contributions of all kinds.

Prof. Dr. J. Peter W. Young
Guest Editor

Keywords

  • bacteria
  • genomics
  • genome evolution
  • chromosome
  • plasmid
  • chromid
  • mobile elements
  • horizontal gene transfer
  • core genome
  • pangenome
  • accessory genes

Published Papers (9 papers)

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Research

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Open AccessArticle Genome Sequence of Azospirillum brasilense CBG497 and Comparative Analyses of Azospirillum Core and Accessory Genomes provide Insight into Niche Adaptation
Genes 2012, 3(4), 576-602; doi:10.3390/genes3040576
Received: 14 May 2012 / Revised: 24 August 2012 / Accepted: 13 September 2012 / Published: 28 September 2012
Cited by 11 | PDF Full-text (360 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Bacteria of the genus Azospirillum colonize roots of important cereals and grasses, and promote plant growth by several mechanisms, notably phytohormone synthesis. The genomes of several Azospirillum strains belonging to different species, isolated from various host plants and locations, were recently sequenced and
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Bacteria of the genus Azospirillum colonize roots of important cereals and grasses, and promote plant growth by several mechanisms, notably phytohormone synthesis. The genomes of several Azospirillum strains belonging to different species, isolated from various host plants and locations, were recently sequenced and published. In this study, an additional genome of an A. brasilense strain, isolated from maize grown on an alkaline soil in the northeast of Mexico, strain CBG497, was obtained. Comparative genomic analyses were performed on this new genome and three other genomes (A. brasilense Sp245, A. lipoferum 4B and Azospirillum sp. B510). The Azospirillum core genome was established and consists of 2,328 proteins, representing between 30% to 38% of the total encoded proteins within a genome. It is mainly chromosomally-encoded and contains 74% of genes of ancestral origin shared with some aquatic relatives. The non-ancestral part of the core genome is enriched in genes involved in signal transduction, in transport and in metabolism of carbohydrates and amino-acids, and in surface properties features linked to adaptation in fluctuating environments, such as soil and rhizosphere. Many genes involved in colonization of plant roots, plant-growth promotion (such as those involved in phytohormone biosynthesis), and properties involved in rhizosphere adaptation (such as catabolism of phenolic compounds, uptake of iron) are restricted to a particular strain and/or species, strongly suggesting niche-specific adaptation. Full article
(This article belongs to the Special Issue Bacterial Genomes and Their Evolution)
Open AccessCommunication A Gene-By-Gene Approach to Bacterial Population Genomics: Whole Genome MLST of Campylobacter
Genes 2012, 3(2), 261-277; doi:10.3390/genes3020261
Received: 1 March 2012 / Revised: 30 March 2012 / Accepted: 31 March 2012 / Published: 12 April 2012
Cited by 24 | PDF Full-text (500 KB) | HTML Full-text | XML Full-text
Abstract
Campylobacteriosis remains a major human public health problem world-wide. Genetic analyses of Campylobacter isolates, and particularly molecular epidemiology, have been central to the study of this disease, particularly the characterization of Campylobacter genotypes isolated from human infection, farm animals, and retail food. These
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Campylobacteriosis remains a major human public health problem world-wide. Genetic analyses of Campylobacter isolates, and particularly molecular epidemiology, have been central to the study of this disease, particularly the characterization of Campylobacter genotypes isolated from human infection, farm animals, and retail food. These studies have demonstrated that Campylobacter populations are highly structured, with distinct genotypes associated with particular wild or domestic animal sources, and that chicken meat is the most likely source of most human infection in countries such as the UK. The availability of multiple whole genome sequences from Campylobacter isolates presents the prospect of identifying those genes or allelic variants responsible for host-association and increased human disease risk, but the diversity of Campylobacter genomes present challenges for such analyses. We present a gene-by-gene approach for investigating the genetic basis of phenotypes in diverse bacteria such as Campylobacter, implemented with the BIGSdb software on the pubMLST.org/campylobacter website. Full article
(This article belongs to the Special Issue Bacterial Genomes and Their Evolution)
Open AccessArticle The Genetics of Symbiotic Nitrogen Fixation: Comparative Genomics of 14 Rhizobia Strains by Resolution of Protein Clusters
Genes 2012, 3(1), 138-166; doi:10.3390/genes3010138
Received: 24 January 2012 / Revised: 10 February 2012 / Accepted: 13 February 2012 / Published: 16 February 2012
Cited by 15 | PDF Full-text (526 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The symbiotic relationship between legumes and nitrogen fixing bacteria is critical for agriculture, as it may have profound impacts on lowering costs for farmers, on land sustainability, on soil quality, and on mitigation of greenhouse gas emissions. However, despite the importance of the
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The symbiotic relationship between legumes and nitrogen fixing bacteria is critical for agriculture, as it may have profound impacts on lowering costs for farmers, on land sustainability, on soil quality, and on mitigation of greenhouse gas emissions. However, despite the importance of the symbioses to the global nitrogen cycling balance, very few rhizobial genomes have been sequenced so far, although there are some ongoing efforts in sequencing elite strains. In this study, the genomes of fourteen selected strains of the order Rhizobiales, all previously fully sequenced and annotated, were compared to assess differences between the strains and to investigate the feasibility of defining a core ‘symbiome’—the essential genes required by all rhizobia for nodulation and nitrogen fixation. Comparison of these whole genomes has revealed valuable information, such as several events of lateral gene transfer, particularly in the symbiotic plasmids and genomic islands that have contributed to a better understanding of the evolution of contrasting symbioses. Unique genes were also identified, as well as omissions of symbiotic genes that were expected to be found. Protein comparisons have also allowed the identification of a variety of similarities and differences in several groups of genes, including those involved in nodulation, nitrogen fixation, production of exopolysaccharides, Type I to Type VI secretion systems, among others, and identifying some key genes that could be related to host specificity and/or a better saprophytic ability. However, while several significant differences in the type and number of proteins were observed, the evidence presented suggests no simple core symbiome exists. A more abstract systems biology concept of nitrogen fixing symbiosis may be required. The results have also highlighted that comparative genomics represents a valuable tool for capturing specificities and generalities of each genome. Full article
(This article belongs to the Special Issue Bacterial Genomes and Their Evolution)
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Open AccessArticle Comparative Genomics of Aeschynomene Symbionts: Insights into the Ecological Lifestyle of Nod-Independent Photosynthetic Bradyrhizobia
Genes 2012, 3(1), 35-61; doi:10.3390/genes3010035
Received: 16 September 2011 / Revised: 8 November 2011 / Accepted: 23 November 2011 / Published: 21 December 2011
Cited by 8 | PDF Full-text (1949 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Tropical aquatic species of the legume genus Aeschynomene are stem- and root-nodulated by bradyrhizobia strains that exhibit atypical features such as photosynthetic capacities or the use of a nod gene-dependent (ND) or a nod gene-independent (NI) pathway to enter into symbiosis with legumes.
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Tropical aquatic species of the legume genus Aeschynomene are stem- and root-nodulated by bradyrhizobia strains that exhibit atypical features such as photosynthetic capacities or the use of a nod gene-dependent (ND) or a nod gene-independent (NI) pathway to enter into symbiosis with legumes. In this study we used a comparative genomics approach on nine Aeschynomene symbionts representative of their phylogenetic diversity. We produced draft genomes of bradyrhizobial strains representing different phenotypes: five NI photosynthetic strains (STM3809, ORS375, STM3847, STM4509 and STM4523) in addition to the previously sequenced ORS278 and BTAi1 genomes, one photosynthetic strain ORS285 hosting both ND and NI symbiotic systems, and one NI non-photosynthetic strain (STM3843). Comparative genomics allowed us to infer the core, pan and dispensable genomes of Aeschynomene bradyrhizobia, and to detect specific genes and their location in Genomic Islands (GI). Specific gene sets linked to photosynthetic and NI/ND abilities were identified, and are currently being studied in functional analyses. Full article
(This article belongs to the Special Issue Bacterial Genomes and Their Evolution)
Open AccessArticle Plant-Bacteria Association and Symbiosis: Are There Common Genomic Traits in Alphaproteobacteria?
Genes 2011, 2(4), 1017-1032; doi:10.3390/genes2041017
Received: 29 September 2011 / Revised: 8 November 2011 / Accepted: 9 November 2011 / Published: 29 November 2011
Cited by 18 | PDF Full-text (529 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Alphaproteobacteria show a great versatility in adapting to a broad range of environments and lifestyles, with the association between bacteria and plants as one of the most intriguing, spanning from relatively unspecific nonsymbiotic association (as rhizospheric or endophytic strains) to the highly species-specific
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Alphaproteobacteria show a great versatility in adapting to a broad range of environments and lifestyles, with the association between bacteria and plants as one of the most intriguing, spanning from relatively unspecific nonsymbiotic association (as rhizospheric or endophytic strains) to the highly species-specific interaction of rhizobia. To shed some light on possible common genetic features in such a heterogeneous set of plant associations, the genomes of 92 Alphaproteobacteria strains were analyzed with a fuzzy orthologs-species detection approach. This showed that the different habitats and lifestyles of plant-associated bacteria (soil, plant colonizers, symbiont) are partially reflected by the trend to have larger genomes with respect to nonplant-associated species. A relatively large set of genes specific to symbiotic bacteria (73 orthologous groups) was found, with a remarkable presence of regulators, sugar transporters, metabolic enzymes, nodulation genes and several genes with unknown function that could be good candidates for further characterization. Interestingly, 15 orthologous groupspresent in all plant-associated bacteria (symbiotic and nonsymbiotic), but absent in nonplant-associated bacteria, were also found, whose functions were mainly related to regulation of gene expression and electron transport. Two of these orthologous groups were also detected in fully sequenced plant-associated Betaproteobacteria and Gammaproteobacteria. Overall these results lead us to hypothesize that plant-bacteria associations, though quite variable, are partially supported by a conserved set of unsuspected gene functions. Full article
(This article belongs to the Special Issue Bacterial Genomes and Their Evolution)
Open AccessArticle Conservation and Occurrence of Trans-Encoded sRNAs in the Rhizobiales
Genes 2011, 2(4), 925-956; doi:10.3390/genes2040925
Received: 31 August 2011 / Revised: 24 October 2011 / Accepted: 26 October 2011 / Published: 18 November 2011
Cited by 10 | PDF Full-text (1212 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Post-transcriptional regulation by trans-encoded sRNAs, for example via base-pairing with target mRNAs, is a common feature in bacteria and influences various cell processes, e.g., response to stress factors. Several studies based on computational and RNA-seq approaches identified approximately 180 trans-encoded sRNAs in Sinorhizobium
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Post-transcriptional regulation by trans-encoded sRNAs, for example via base-pairing with target mRNAs, is a common feature in bacteria and influences various cell processes, e.g., response to stress factors. Several studies based on computational and RNA-seq approaches identified approximately 180 trans-encoded sRNAs in Sinorhizobium meliloti. The initial point of this report is a set of 52 trans-encoded sRNAs derived from the former studies. Sequence homology combined with structural conservation analyses were applied to elucidate the occurrence and distribution of conserved trans-encoded sRNAs in the order of Rhizobiales. This approach resulted in 39 RNA family models (RFMs) which showed various taxonomic distribution patterns. Whereas the majority of RFMs was restricted to Sinorhizobium species or the Rhizobiaceae, members of a few RFMs were more widely distributed in the Rhizobiales. Access to this data is provided via the RhizoGATE portal [1,2]. Full article
(This article belongs to the Special Issue Bacterial Genomes and Their Evolution)
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Open AccessArticle Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T
Genes 2011, 2(4), 763-787; doi:10.3390/genes2040763
Received: 7 September 2011 / Revised: 11 October 2011 / Accepted: 12 October 2011 / Published: 28 October 2011
Cited by 23 | PDF Full-text (1049 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The complete nucleotide sequence of the genome of the soybean symbiont Bradyrhizobium japonicum strain USDA6T was determined. The genome of USDA6T is a single circular chromosome of 9,207,384 bp. The genome size is similar to that of the genome of another
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The complete nucleotide sequence of the genome of the soybean symbiont Bradyrhizobium japonicum strain USDA6T was determined. The genome of USDA6T is a single circular chromosome of 9,207,384 bp. The genome size is similar to that of the genome of another soybean symbiont, B. japonicum USDA110 (9,105,828 bp). Comparison of the whole-genome sequences of USDA6T and USDA110 showed colinearity of major regions in the two genomes, although a large inversion exists between them. A significantly high level of sequence conservation was detected in three regions on each genome. The gene constitution and nucleotide sequence features in these three regions indicate that they may have been derived from a symbiosis island. An ancestral, large symbiosis island, approximately 860 kb in total size, appears to have been split into these three regions by unknown large-scale genome rearrangements. The two integration events responsible for this appear to have taken place independently, but through comparable mechanisms, in both genomes. Full article
(This article belongs to the Special Issue Bacterial Genomes and Their Evolution)

Review

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Open AccessReview From Environment to Man: Genome Evolution and Adaptation of Human Opportunistic Bacterial Pathogens
Genes 2012, 3(2), 191-232; doi:10.3390/genes3020191
Received: 2 February 2012 / Revised: 29 February 2012 / Accepted: 29 February 2012 / Published: 26 March 2012
Cited by 10 | PDF Full-text (890 KB) | HTML Full-text | XML Full-text
Abstract
Environment is recognized as a huge reservoir for bacterial species and a source of human pathogens. Some environmental bacteria have an extraordinary range of activities that include promotion of plant growth or disease, breakdown of pollutants, production of original biomolecules, but also multidrug
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Environment is recognized as a huge reservoir for bacterial species and a source of human pathogens. Some environmental bacteria have an extraordinary range of activities that include promotion of plant growth or disease, breakdown of pollutants, production of original biomolecules, but also multidrug resistance and human pathogenicity. The versatility of bacterial life-style involves adaptation to various niches. Adaptation to both open environment and human specific niches is a major challenge that involves intermediate organisms allowing pre-adaptation to humans. The aim of this review is to analyze genomic features of environmental bacteria in order to explain their adaptation to human beings. The genera Pseudomonas, Aeromonas and Ochrobactrum provide valuable examples of opportunistic behavior associated to particular genomic structure and evolution. Particularly, we performed original genomic comparisons among aeromonads and between the strictly intracellular pathogens Brucella spp. and the mild opportunistic pathogens Ochrobactrum spp. We conclude that the adaptation to human could coincide with a speciation in action revealed by modifications in both genomic and population structures. This adaptation-driven speciation could be a major mechanism for the emergence of true pathogens besides the acquisition of specialized virulence factors. Full article
(This article belongs to the Special Issue Bacterial Genomes and Their Evolution)
Open AccessReview Ecological and Temporal Constraints in the Evolution of Bacterial Genomes
Genes 2011, 2(4), 804-828; doi:10.3390/genes2040804
Received: 14 September 2011 / Revised: 10 October 2011 / Accepted: 24 October 2011 / Published: 31 October 2011
Cited by 7 | PDF Full-text (523 KB) | HTML Full-text | XML Full-text
Abstract
Studies on the experimental evolution of microorganisms, on their in vivo evolution (mainly in the case of bacteria producing chronic infections), as well as the availability of multiple full genomic sequences, are placing bacteria in the playground of evolutionary studies. In the present
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Studies on the experimental evolution of microorganisms, on their in vivo evolution (mainly in the case of bacteria producing chronic infections), as well as the availability of multiple full genomic sequences, are placing bacteria in the playground of evolutionary studies. In the present article we review the differential contribution to the evolution of bacterial genomes that processes such as gene modification, gene acquisition and gene loss may have when bacteria colonize different habitats that present characteristic ecological features. In particular, we review how the different processes contribute to evolution in microbial communities, in free-living bacteria or in bacteria living in isolation. In addition, we discuss the temporal constraints in the evolution of bacterial genomes, considering bacterial evolution from the perspective of processes of short-sighted evolution and punctual acquisition of evolutionary novelties followed by long stasis periods. Full article
(This article belongs to the Special Issue Bacterial Genomes and Their Evolution)

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