Special Issue "Bacterial Genomes and Their Evolution"

Guest Editor
Prof. Dr. J. Peter W. Young
Department of Biology, University of York, Heslington, York YO10 5DD, UK
Website: http://www.york.ac.uk/biology/research/ecology-evolution/j-peter-w-young/
E-Mail: jpy1@york.ac.uk
Phone: +44 1904 328630
Fax: +44 1904 328505
Interests: bacterial genomes; population genetics; phylogenomics; phylogenetics; genome projects; genetic diversity

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

Submission

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

Type of Paper: Article
Title: Complete Genome Sequence of A Soybean Symbiont Bradyrhizobium Japonicum Strain USDA6
Author: Takakazu Kaneko
Affiliation: Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto-City 603-8555, Japan; E-Mail: tkaneko@cc.kyoto-su.ac.jp
Abstract: The nucleotide sequence of a soybean symbiont Bradyrhizobium japonicum USDA6 was determined. The chromosomally integrated elements were predicted by comparing with B. japonicum USDA110 genome. One of them was identified as a symbiosis island with a length of 693 kb. The island is flanked by a valine-tRNA gene as is the case in the USDA110 genome. The islands from two strains, USDA6 and USDA110, share approximately 600 kb of DNA regions in which the nucleotide level identity is significantly higher compare to the identity in the genomic backbone. The closely related nucleotide sequences show that the symbiosis islands of two soybean symbionts would be acquired recently by lateral transfer process.

Type of Paper: Review
Title: Ecological and Temporal Constrains in the Evolution of Bacterial Genomes
Authors: Luis Boto ¹ and Jose Luis Martínez ²
Affiliations: ¹ Dpto Biodiversidad y Biología Evolutiva, Museo Nacional Ciencias Naturales, CSIC, Madrid, Spain
² Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Madrid, Spain
Abstract: Gene modification, gene acquisition and gene loss modulate genomes evolution in bacteria. This review is focused in the relative contribution of these processes in different ecological conditions. In particular, we review how the different processes do contribute to genomes evolution in free living bacteria, in bacteria inhabiting closed ecosystems characterized by high diversity, and in endosymbiotic bacteria. In addition, we explore the differential role played by mutation and gene acquisition at long and short  term (short-seeing) evolution.

Type of Paper: Article
Title: Occurrence and Distribution of Conserved sRNAs in the Rhizobiales
Authors: Jan-Philip Schlüter ¹, Jan Reinkensmeier ², Anke Becker ¹ and Robert Giegerich ²
Affiliation: ¹ Faculty of Biology, University of Freiburg, Germany; E-Mail: anke.becker@biologie.uni-freiburg.de (A.B.)
² Technical Faculty, Bielefeld University, Germany
Abstract: Post-transcriptional regulation by trans-encoded sRNAs 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 RNAseq approaches identified approximately 200 trans-encoded sRNAs in Sinorhizobium meliloti. In this study a set of trans-encoded sRNAs derived from these previous studies and additionally some new sRNA candidates were used for a comparative study. Sequence homology combined with structural conservation analyses was applied to elucidate the occurrence and distribution of conserved trans-encoded sRNAs in the Rhizobiales.

Type of Paper: Review
Title: From Environment to Man: Genome Evolution and Adaptation of Opportunistic Human Pathogens
Authors: Fabien Aujoulat, Hélène Marchandin and Estelle Jumas-Bilak
Affiliation: Université Montpellier 1, UMR 5119 (UM2, CNRS, IRD, IFREMER, UM1), Équipe Pathogènes et Environnements, Montpellier, France;
E-Mail: ebilak@univ-montp1.fr (E.J.-B.)
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 plant growth or disease, breakdown of pollutants, production of original biomolecules but also multidrug resistance and human pathogenicity. The wide range of activities of versatile life-style bacteria involves adaptation to various niches. It is noteworthy that the adaptation to both open environment and human specific niche is a major challenge. The aim of this review is to analyze genomic features of environmental bacteria mainly belonging to the genera Pseudomonas, Stenotrophomonas, Burkholderia, Ochrobactrum and Agrobacterium in order to explain their adaptation to human beings. Particularly, free-living generalist bacteria have larger genomes than closely related bacteria with specialist behavior. To illustrate this general observation, we compare the genome structure and the gene content of the strictly intracellular pathogens Brucella spp. to those of the mild opportunistic pathogens Ochrobactrum spp. Finally, genomic data will be considered in the light of the population structure of the corresponding species or genera. Populations of versatile opportunistic pathogens are structured in clonal complexes rather than in delineated “true” species. 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 beside the acquisition of specialized virulence factors.