2
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Cao S, Brandis G, Huseby DL, Hughes D. Positive selection during niche adaptation results in large-scale and irreversible rearrangement of chromosomal gene order in bacteria. Mol Biol Evol 2022; 39:6554941. [PMID: 35348727 PMCID: PMC9016547 DOI: 10.1093/molbev/msac069] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Analysis of bacterial genomes shows that, whereas diverse species share many genes in common, their linear order on the chromosome is often not conserved. Whereas rearrangements in gene order could occur by genetic drift, an alternative hypothesis is rearrangement driven by positive selection during niche adaptation (SNAP). Here, we provide the first experimental support for the SNAP hypothesis. We evolved Salmonella to adapt to growth on malate as the sole carbon source and followed the evolutionary trajectories. The initial adaptation to growth in the new environment involved the duplication of 1.66 Mb, corresponding to one-third of the Salmonella chromosome. This duplication is selected to increase the copy number of a single gene, dctA, involved in the uptake of malate. Continuing selection led to the rapid loss or mutation of duplicate genes from either copy of the duplicated region. After 2000 generations, only 31% of the originally duplicated genes remained intact and the gene order within the Salmonella chromosome has been significantly and irreversibly altered. These results experientially validate predictions made by the SNAP hypothesis and show that SNAP can be a strong driving force for rearrangements in chromosomal gene order.
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Affiliation(s)
- Sha Cao
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,These authors contributed equally: Sha Cao, Gerrit Brandis
| | - Gerrit Brandis
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.,These authors contributed equally: Sha Cao, Gerrit Brandis
| | - Douglas L Huseby
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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4
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Stanton E, Wahlig TA, Park D, Kaspar CW. Chronological set of E. coli O157:H7 bovine strains establishes a role for repeat sequences and mobile genetic elements in genome diversification. BMC Genomics 2020; 21:562. [PMID: 32807088 PMCID: PMC7430833 DOI: 10.1186/s12864-020-06943-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/23/2020] [Indexed: 11/21/2022] Open
Abstract
Background Enterohemorrhagic Escherichia coli O157:H7 (EHEC) is a significant foodborne pathogen that resides asymptomatically within cattle and other ruminants. The EHEC genome harbors an extensive collection of mobile genetic elements (MGE), including multiple prophage, prophage-like elements, plasmids, and insertion sequence (IS) elements. Results A chronological collection of EHEC strains (FRIK804, FRIK1275, and FRIK1625) isolated from a Wisconsin dairy farm (farm X) comprised a closely related clade genetically differentiated by structural alterations to the chromosome. Comparison of the FRIK804 genome with a reference EHEC strain Sakai found a unique prophage like element (PLE, indel 1) and an inversion (1.15 Mb) situated symmetrically with respect to the terminus region. Detailed analysis determined the inversion was due to homologous recombination between repeat sequences in prophage. The three farm X strains were distinguished by the presence or absence of indel 3 (61 kbp) and indel 4 (48 kbp); FRIK804 contained both of these regions, FRIK1275 lacked indel 4, and indels 3 and 4 were both absent in FRIK1625. Indel 3 was the stx2 prophage and indel 4 involved a deletion between two adjacent prophage with shared repeat sequences. Both FRIK804 and FRIK1275 produced functional phage while FRIK1625 did not, which is consistent with indel 3. Due to their involvement in recombination events, direct and inverted repeat sequences were identified, and their locations mapped to the chromosome. FRIK804 had a greater number and overall length of repeat sequences than E. coli K12 strain MG1655. Repeat sequences were most commonly associated with MGE. Conclusions This research demonstrated that three EHEC strains from a Wisconsin dairy farm were closely related and distinguished by variability within prophage regions and other MGE. Chromosome alterations were associated with recombination events between repeat sequences. An inventory of direct and inverted repeat sequences found a greater abundance and total length of repeat sequences in the EHEC strains compared to E. coli strain MG1655. The locations of the repeat sequences were biased towards MGE. The findings from this study expand our understanding of the precise molecular events and elements that contributed to genetic diversification of wild-type EHEC in the bovine and farm environments.
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Affiliation(s)
- Eliot Stanton
- Department of Bacteriology, University of Wisconsin-Madison, Microbial Sciences Building, 1550 Linden Drive, Madison, WI, 53706, USA
| | - Taylor A Wahlig
- Department of Bacteriology, University of Wisconsin-Madison, Microbial Sciences Building, 1550 Linden Drive, Madison, WI, 53706, USA.,University of Utah, School of Medicine, 30 N 1900 E, Salt Lake City, UT, 84132, USA
| | - Dongjin Park
- Food Science and Technology Department, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Charles W Kaspar
- Department of Bacteriology, University of Wisconsin-Madison, Microbial Sciences Building, 1550 Linden Drive, Madison, WI, 53706, USA. .,Food Research Institute, University of Wisconsin-Madison, Microbial Sciences Building, 1550 Linden Drive, Madison, WI, 53706, USA.
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5
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Cole LW, Guo W, Mower JP, Palmer JD. High and Variable Rates of Repeat-Mediated Mitochondrial Genome Rearrangement in a Genus of Plants. Mol Biol Evol 2019; 35:2773-2785. [PMID: 30202905 DOI: 10.1093/molbev/msy176] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
For 30 years, it has been clear that angiosperm mitochondrial genomes evolve rapidly in sequence arrangement (i.e., synteny), yet absolute rates of rearrangement have not been measured in any plant group, nor is it known how much these rates vary. To investigate these issues, we sequenced and reconstructed the rearrangement history of seven mitochondrial genomes in Monsonia (Geraniaceae). We show that rearrangements (occurring mostly as inversions) not only take place at generally high rates in these genomes but also uncover significant variation in rearrangement rates. For example, the hyperactive mitochondrial genome of Monsonia ciliata has accumulated at least 30 rearrangements over the last million years, whereas the branch leading to M. ciliata and its sister species has sustained rearrangement at a rate that is at least ten times lower. Furthermore, our analysis of published data shows that rates of mitochondrial genome rearrangement in seed plants vary by at least 600-fold. We find that sites of rearrangement are highly preferentially located in very close proximity to repeated sequences in Monsonia. This provides strong support for the hypothesis that rearrangement in angiosperm mitochondrial genomes occurs largely through repeat-mediated recombination. Because there is little variation in the amount of repeat sequence among Monsonia genomes, the variable rates of rearrangement in Monsonia probably reflect variable rates of mitochondrial recombination itself. Finally, we show that mitochondrial synonymous substitutions occur in a clock-like manner in Monsonia; rates of mitochondrial substitutions and rearrangements are therefore highly uncoupled in this group.
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Affiliation(s)
- Logan W Cole
- Department of Biology, Indiana University, Bloomington, IN
| | | | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE.,Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE
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6
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Shelyakin PV, Bochkareva OO, Karan AA, Gelfand MS. Micro-evolution of three Streptococcus species: selection, antigenic variation, and horizontal gene inflow. BMC Evol Biol 2019; 19:83. [PMID: 30917781 PMCID: PMC6437910 DOI: 10.1186/s12862-019-1403-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/25/2019] [Indexed: 02/07/2023] Open
Abstract
Background The genus Streptococcus comprises pathogens that strongly influence the health of humans and animals. Genome sequencing of multiple Streptococcus strains demonstrated high variability in gene content and order even in closely related strains of the same species and created a newly emerged object for genomic analysis, the pan-genome. Here we analysed the genome evolution of 25 strains of Streptococcus suis, 50 strains of Streptococcus pyogenes and 28 strains of Streptococcus pneumoniae. Results Fractions of the pan-genome, unique, periphery, and universal genes differ in size, functional composition, the level of nucleotide substitutions, and predisposition to horizontal gene transfer and genomic rearrangements. The density of substitutions in intergenic regions appears to be correlated with selection acting on adjacent genes, implying that more conserved genes tend to have more conserved regulatory regions. The total pan-genome of the genus is open, but only due to strain-specific genes, whereas other pan-genome fractions reach saturation. We have identified the set of genes with phylogenies inconsistent with species and non-conserved location in the chromosome; these genes are rare in at least one species and have likely experienced recent horizontal transfer between species. The strain-specific fraction is enriched with mobile elements and hypothetical proteins, but also contains a number of candidate virulence-related genes, so it may have a strong impact on adaptability and pathogenicity. Mapping the rearrangements to the phylogenetic tree revealed large parallel inversions in all species. A parallel inversion of length 15 kB with breakpoints formed by genes encoding surface antigen proteins PhtD and PhtB in S. pneumoniae leads to replacement of gene fragments that likely indicates the action of an antigen variation mechanism. Conclusions Members of genus Streptococcus have a highly dynamic, open pan-genome, that potentially confers them with the ability to adapt to changing environmental conditions, i.e. antibiotic resistance or transmission between different hosts. Hence, integrated analysis of all aspects of genome evolution is important for the identification of potential pathogens and design of drugs and vaccines. Electronic supplementary material The online version of this article (10.1186/s12862-019-1403-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pavel V Shelyakin
- Vavilov Institute of General Genetics Russian Academy of Sciences, Gubkina str. 3, Moscow, 119991, Russia. .,Kharkevich Institute for Information Transmission Problems, 19, Bolshoy Karetny per., Moscow, 127051, Russia. .,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.
| | - Olga O Bochkareva
- Kharkevich Institute for Information Transmission Problems, 19, Bolshoy Karetny per., Moscow, 127051, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Anna A Karan
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail S Gelfand
- Kharkevich Institute for Information Transmission Problems, 19, Bolshoy Karetny per., Moscow, 127051, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Faculty of Computer Science, Higher School of Economics, Moscow, Russia
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7
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Peng Y, Tang S, Wang D, Zhong H, Jia H, Cai X, Zhang Z, Xiao M, Yang H, Wang J, Kristiansen K, Xu X, Li J. MetaPGN: a pipeline for construction and graphical visualization of annotated pangenome networks. Gigascience 2018; 7:5114262. [PMID: 30277499 PMCID: PMC6251982 DOI: 10.1093/gigascience/giy121] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 09/20/2018] [Indexed: 02/01/2023] Open
Abstract
Pangenome analyses facilitate the interpretation of genetic diversity and evolutionary history of a taxon. However, there is an urgent and unmet need to develop new tools for advanced pangenome construction and visualization, especially for metagenomic data. Here, we present an integrated pipeline, named MetaPGN, for construction and graphical visualization of pangenome networks from either microbial genomes or metagenomes. Given either isolated genomes or metagenomic assemblies coupled with a reference genome of the targeted taxon, MetaPGN generates a pangenome in a topological network, consisting of genes (nodes) and gene-gene genomic adjacencies (edges) of which biological information can be easily updated and retrieved. MetaPGN also includes a self-developed Cytoscape plugin for layout of and interaction with the resulting pangenome network, providing an intuitive and interactive interface for full exploration of genetic diversity. We demonstrate the utility of MetaPGN by constructing Escherichia coli pangenome networks from five E. coli pathogenic strains and 760 human gut microbiomes,revealing extensive genetic diversity of E. coli within both isolates and gut microbial populations. With the ability to extract and visualize gene contents and gene-gene physical adjacencies of a specific taxon from large-scale metagenomic data, MetaPGN provides advantages in expanding pangenome analysis to uncultured microbial taxa.
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Affiliation(s)
- Ye Peng
- School of Biology and Biological Engineering, South China University of Technology, Building B6, 382 Zhonghuan Road East, Guangzhou Higher Education Mega Center, Guangzhou 510006, China.,BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Dapeng New District, Shenzhen 518120, China
| | - Shanmei Tang
- BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Dapeng New District, Shenzhen 518120, China.,Shenzhen Key Laboratory of Human commensal microorganisms and Health Research, BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian, Shenzhen 518083, China
| | - Dan Wang
- BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Dapeng New District, Shenzhen 518120, China.,Shenzhen Key Laboratory of Human commensal microorganisms and Health Research, BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian, Shenzhen 518083, China
| | - Huanzi Zhong
- BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Dapeng New District, Shenzhen 518120, China.,Shenzhen Key Laboratory of Human commensal microorganisms and Health Research, BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian, Shenzhen 518083, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen Biocenter, Ole MaalØes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Huijue Jia
- BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Dapeng New District, Shenzhen 518120, China.,Shenzhen Key Laboratory of Human commensal microorganisms and Health Research, BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian, Shenzhen 518083, China
| | - Xianghang Cai
- BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Dapeng New District, Shenzhen 518120, China
| | - Zhaoxi Zhang
- BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Dapeng New District, Shenzhen 518120, China
| | - Minfeng Xiao
- BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Dapeng New District, Shenzhen 518120, China
| | - Huanming Yang
- BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, No. 51, Zhijiang Road, Xihu District, Hangzhou 310058, China
| | - Jian Wang
- BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, No. 51, Zhijiang Road, Xihu District, Hangzhou 310058, China
| | - Karsten Kristiansen
- BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Dapeng New District, Shenzhen 518120, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen Biocenter, Ole MaalØes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Xun Xu
- BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Dapeng New District, Shenzhen 518120, China
| | - Junhua Li
- School of Biology and Biological Engineering, South China University of Technology, Building B6, 382 Zhonghuan Road East, Guangzhou Higher Education Mega Center, Guangzhou 510006, China.,BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Dapeng New District, Shenzhen 518120, China.,Shenzhen Key Laboratory of Human commensal microorganisms and Health Research, BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian, Shenzhen 518083, China
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