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      Pan-genome analyses of 24 Shewanella strains re-emphasize the diversification of their functions yet evolutionary dynamics of metal-reducing pathway

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          Abstract

          Background

          Shewanella strains are important dissimilatory metal-reducing bacteria which are widely distributed in diverse habitats. Despite efforts to genomically characterize Shewanella, knowledge of the molecular components, functional information and evolutionary patterns remain lacking, especially for their compatibility in the metal-reducing pathway. The increasing number of genome sequences of Shewanella strains offers a basis for pan-genome studies.

          Results

          A comparative pan-genome analysis was conducted to study genomic diversity and evolutionary relationships among 24 Shewanella strains. Results revealed an open pan-genome of 13,406 non-redundant genes and a core-genome of 1878 non-redundant genes. Selective pressure acted on the invariant members of core genome, in which purifying selection drove evolution in the housekeeping mechanisms. Shewanella strains exhibited extensive genome variability, with high levels of gene gain and loss during the evolution, which affected variable gene sets and facilitated the rapid evolution. Additionally, genes related to metal reduction were diversely distributed in Shewanella strains and evolved under purifying selection, which highlighted the basic conserved functionality and specificity of respiratory systems.

          Conclusions

          The diversity of genes present in the accessory and specific genomes of Shewanella strains indicates that each strain uses different strategies to adapt to diverse environments. Horizontal gene transfer is an important evolutionary force in shaping Shewanella genomes. Purifying selection plays an important role in the stability of the core-genome and also drives evolution in mtr– omc cluster of different Shewanella strains.

          Electronic supplementary material

          The online version of this article (10.1186/s13068-018-1201-1) contains supplementary material, which is available to authorized users.

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          Electrically conductive bacterial nanowires produced by Shewanella oneidensis strain MR-1 and other microorganisms.

          Yuri A. Gorby, Svetlana Yanina, Jeffrey S McLean … (2006)
          Shewanella oneidensis MR-1 produced electrically conductive pilus-like appendages called bacterial nanowires in direct response to electron-acceptor limitation. Mutants deficient in genes for c-type decaheme cytochromes MtrC and OmcA, and those that lacked a functional Type II secretion pathway displayed nanowires that were poorly conductive. These mutants were also deficient in their ability to reduce hydrous ferric oxide and in their ability to generate current in a microbial fuel cell. Nanowires produced by the oxygenic phototrophic cyanobacterium Synechocystis PCC6803 and the thermophilic, fermentative bacterium Pelotomaculum thermopropionicum reveal that electrically conductive appendages are not exclusive to dissimilatory metal-reducing bacteria and may, in fact, represent a common bacterial strategy for efficient electron transfer and energy distribution.
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            De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits.

            Ying-Hui Li, Guangyu Zhou, Jianxin Ma … (2014)
            Wild relatives of crops are an important source of genetic diversity for agriculture, but their gene repertoire remains largely unexplored. We report the establishment and analysis of a pan-genome of Glycine soja, the wild relative of cultivated soybean Glycine max, by sequencing and de novo assembly of seven phylogenetically and geographically representative accessions. Intergenomic comparisons identified lineage-specific genes and genes with copy number variation or large-effect mutations, some of which show evidence of positive selection and may contribute to variation of agronomic traits such as biotic resistance, seed composition, flowering and maturity time, organ size and final biomass. Approximately 80% of the pan-genome was present in all seven accessions (core), whereas the rest was dispensable and exhibited greater variation than the core genome, perhaps reflecting a role in adaptation to diverse environments. This work will facilitate the harnessing of untapped genetic diversity from wild soybean for enhancement of elite cultivars.
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              Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis.

              Ana Moran, H Ochman (2001)
              Traditionally, evolutionary biologists have viewed mutations within individual genes as the major source of phenotypic variation leading to adaptation through natural selection, and ultimately generating diversity among species. Although such processes must contribute to the initial development of gene functions and their subsequent fine-tuning, changes in genome repertoire, occurring through gene acquisition and deletion, are the major events underlying the emergence and evolution of bacterial pathogens and symbionts. Furthermore, pathogens and symbionts depend on similar mechanisms for interacting with hosts and show parallel trends in genome evolution.
              Article 0 comments Cited 157 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Kang Ning: 86-27-87793041 , ningkang@hust.edu.cn
                Journal
                Journal ID (nlm-ta): Biotechnol Biofuels
                Journal ID (iso-abbrev): Biotechnol Biofuels
                Title: Biotechnology for Biofuels
                Publisher: BioMed Central (London )
                ISSN (Electronic): 1754-6834
                Publication date (Electronic): 17 July 2018
                Publication date PMC-release: 17 July 2018
                Publication date Collection: 2018
                Volume: 11
                Electronic Location Identifier: 193
                Affiliations
                ISNI 0000 0004 0368 7223, GRID grid.33199.31, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, , Huazhong University of Science and Technology, ; 1037 Luoyu Road, Wuhan, 430074 Hubei China
                Article
                Publisher ID: 1201
                DOI: 10.1186/s13068-018-1201-1
                PMC ID: 6048853
                PubMed ID: 30026808
                SO-VID: f99f5b22-ed98-4760-a420-516a7fdab001
                Copyright © © The Author(s) 2018
                License:

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                Date received : 28 April 2018
                Date accepted : 10 July 2018
                Categories
                Subject: Research
                Custom metadata
                issue-copyright-statement © The Author(s) 2018

                ScienceOpen disciplines: Biotechnology
                Keywords: pan-genome,shewanella,metal-reducing,evolution
                Data availability:
                ScienceOpen disciplines: Biotechnology
                Keywords: pan-genome, shewanella, metal-reducing, evolution

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