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Tam YL, Cameron S, Preston A, Cowley L. GWarrange: a pre- and post- genome-wide association studies pipeline for detecting phenotype-associated genome rearrangement events. Microb Genom 2024; 10. [PMID: 38980151 DOI: 10.1099/mgen.0.001268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024] Open
Abstract
The use of k-mers to capture genetic variation in bacterial genome-wide association studies (bGWAS) has demonstrated its effectiveness in overcoming the plasticity of bacterial genomes by providing a comprehensive array of genetic variants in a genome set that is not confined to a single reference genome. However, little attempt has been made to interpret k-mers in the context of genome rearrangements, partly due to challenges in the exhaustive and high-throughput identification of genome structure and individual rearrangement events. Here, we present GWarrange, a pre- and post-bGWAS processing methodology that leverages the unique properties of k-mers to facilitate bGWAS for genome rearrangements. Repeat sequences are common instigators of genome rearrangements through intragenomic homologous recombination, and they are commonly found at rearrangement boundaries. Using whole-genome sequences, repeat sequences are replaced by short placeholder sequences, allowing the regions flanking repeats to be incorporated into relatively short k-mers. Then, locations of flanking regions in significant k-mers are mapped back to complete genome sequences to visualise genome rearrangements. Four case studies based on two bacterial species (Bordetella pertussis and Enterococcus faecium) and a simulated genome set are presented to demonstrate the ability to identify phenotype-associated rearrangements. GWarrange is available at https://github.com/DorothyTamYiLing/GWarrange.
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Affiliation(s)
- Yi Ling Tam
- The Milner Centre for Evolution and Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Sarah Cameron
- The Milner Centre for Evolution and Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Andrew Preston
- The Milner Centre for Evolution and Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Lauren Cowley
- The Milner Centre for Evolution and Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
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2
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Yang HW, Thapa R, Johnson K, DuPont ST, Khan A, Zhao Y. Examination of Large Chromosomal Inversions in the Genome of Erwinia amylovora Strains Reveals Worldwide Distribution and North America-Specific Types. PHYTOPATHOLOGY 2023; 113:2174-2186. [PMID: 36935376 DOI: 10.1094/phyto-01-23-0004-sa] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Erwinia amylovora is a relatively homogeneous species with low genetic diversity at the nucleotide level. However, phenotypic differences and genomic structural variations among E. amylovora strains have been documented. In this study, we identified 10 large chromosomal inversion (LCI) types in the Spiraeoideae-infecting (SI) E. amylovora strains by combining whole genome sequencing and PCR-based molecular markers. It was found that LCIs were mainly caused by homologous recombination events among seven rRNA operons (rrns) in SI E. amylovora strains. Although ribotyping results identified inter- and intra-variations in the internal transcribed spacer (ITS1 and ITS2) regions among rrns, LCIs tend to occur between rrns transcribed in the opposite directions and with the same tRNA content (tRNA-Glu or tRNA-Ile/Ala) in ITS1. Based on the LCI types, physical/estimated replichore imbalance (PRI/ERI) was examined and calculated. Among the 117 SI strains evaluated, the LCI types of Ea1189, CFBP1430, and Ea273 were the most common, with ERI values at 1.31, 7.87, and 4.47°, respectively. These three LCI types had worldwide distribution, whereas the remaining seven LCI types were restricted to North America (or certain regions of the United States). Our results indicated ongoing chromosomal recombination events in the SI E. amylovora population and showed that LCI events are mostly symmetrical, keeping the ERI less than 15°. These findings provide initial evidence about the prevalence of certain LCI types in E. amylovora strains, how LCI occurs, and its potential evolutionary advantage and history, which might help track the movement of the pathogen.
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Affiliation(s)
- Ho-Wen Yang
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61802
| | - Ranjita Thapa
- School of Integrative Plant Science Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - Kenneth Johnson
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | | | - Awais Khan
- School of Integrative Plant Science Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61802
- Department of Plant Pathology, WSU-IAREC, Prosser, WA 99350
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3
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D’Iorio M, Dewar K. Replication-associated inversions are the dominant form of bacterial chromosome structural variation. Life Sci Alliance 2022; 6:6/1/e202201434. [PMID: 36261227 PMCID: PMC9584773 DOI: 10.26508/lsa.202201434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/24/2022] Open
Abstract
The structural arrangements of bacterial chromosomes vary widely between closely related species and can result in significant phenotypic outcomes. The appearance of large-scale chromosomal inversions that are symmetric relative to markers for the origin of replication (OriC) has been previously observed; however, the overall prevalence of replication-associated structural rearrangements (RASRs) in bacteria and their causal mechanisms are currently unknown. Here, we systematically identify the locations of RASRs in species with multiple complete-sequenced genomes and investigate potential mediating biological mechanisms. We found that 247 of 313 species contained sequences with at least one large (>50 Kb) inversion in their sequence comparisons, and the aggregated inversion distances away from symmetry were normally distributed with a mean of zero. Many inversions that were offset from dnaA were found to be centered on a different marker for the OriC Instances of flanking repeats provide evidence that breaks formed during the replication process could be repaired to opposing positions. We also found a strong relationship between the later stages of replication and the range in distance variation from symmetry.
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Affiliation(s)
- Matthew D’Iorio
- Quantitative Life Sciences, McGill University, Montreal, Canada,Correspondence:
| | - Ken Dewar
- Department of Human Genetics, McGill University, Montreal, Canada,Centre for Microbiome Research, McGill University, Montreal, Canada
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4
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de Sousa KCM, Gutiérrez R, Yahalomi D, Shalit T, Markus B, Nachum-Biala Y, Hawlena H, Marcos-Hadad E, Hazkani-Covo E, de Rezende Neves HH, Covo S, Harrus S. Genomic structural plasticity of rodent-associated Bartonella in nature. Mol Ecol 2022; 31:3784-3797. [PMID: 35620948 PMCID: PMC9540758 DOI: 10.1111/mec.16547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/12/2022] [Accepted: 05/20/2022] [Indexed: 11/28/2022]
Abstract
Rodent‐associated Bartonella species have shown a remarkable genetic diversity and pathogenic potential. To further explore the extent of the natural intraspecific genomic variation and its potential role as an evolutionary driver, we focused on a single genetically diverse Bartonella species, Bartonella krasnovii, which circulates among gerbils and their associated fleas. Twenty genomes from 16 different B. krasnovii genotypes were fully characterized through a genome sequencing assay (using short and long read sequencing), pulse field gel electrophoresis (PFGE), and PCR validation. Genomic analyses were performed in comparison to the B. krasnovii strain OE 1–1. While, single nucleotide polymorphism represented only a 0.3% of the genome variation, structural diversity was identified in these genomes, with an average of 51 ± 24 structural variation (SV) events per genome. Interestingly, a large proportion of the SVs (>40%) was associated with prophages. Further analyses revealed that most of the SVs, and prophage insertions were found at the chromosome replication termination site (ter), suggesting this site as a plastic zone of the B. krasnovii chromosome. Accordingly, six genomes were found to be unbalanced, and essential genes near the ter showed a shift between the leading and lagging strands, revealing the SV effect on these genomes. In summary, our findings demonstrate the extensive genomic diversity harbored by wild B. krasnovii strains and suggests that its diversification is initially promoted by structural changes, probably driven by phages. These events may constantly feed the system with novel genotypes that ultimately lead to inter‐ and intraspecies competition and adaptation.
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Affiliation(s)
| | - Ricardo Gutiérrez
- Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot, Israel.,National Reference Center for Bacteriology. Costa Rican Institute for Research and Teaching in Nutrition and Health (INCIENSA)
| | - Dayana Yahalomi
- The Mantoux Bioinformatics institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Tali Shalit
- The Mantoux Bioinformatics institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Barak Markus
- The Mantoux Bioinformatics institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Yaarit Nachum-Biala
- Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Hadas Hawlena
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Evgeniya Marcos-Hadad
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Einat Hazkani-Covo
- Department of Natural and Life Sciences, Open University of Israel, Raanana, Israel
| | | | - Shay Covo
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shimon Harrus
- Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot, Israel.,National Reference Center for Bacteriology. Costa Rican Institute for Research and Teaching in Nutrition and Health (INCIENSA)
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5
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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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Structure-Aware Mycobacterium tuberculosis Functional Annotation Uncloaks Resistance, Metabolic, and Virulence Genes. mSystems 2021; 6:e0067321. [PMID: 34726489 PMCID: PMC8562490 DOI: 10.1128/msystems.00673-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Accurate and timely functional genome annotation is essential for translating basic pathogen research into clinically impactful advances. Here, through literature curation and structure-function inference, we systematically update the functional genome annotation of Mycobacterium tuberculosis virulent type strain H37Rv. First, we systematically curated annotations for 589 genes from 662 publications, including 282 gene products absent from leading databases. Second, we modeled 1,711 underannotated proteins and developed a semiautomated pipeline that captured shared function between 400 protein models and structural matches of known function on Protein Data Bank, including drug efflux proteins, metabolic enzymes, and virulence factors. In aggregate, these structure- and literature-derived annotations update 940/1,725 underannotated H37Rv genes and generate hundreds of functional hypotheses. Retrospectively applying the annotation to a recent whole-genome transposon mutant screen provided missing function for 48% (13/27) of underannotated genes altering antibiotic efficacy and 33% (23/69) required for persistence during mouse tuberculosis (TB) infection. Prospective application of the protein models enabled us to functionally interpret novel laboratory generated pyrazinamide (PZA)-resistant mutants of unknown function, which implicated the emerging coenzyme A depletion model of PZA action in the mutants’ PZA resistance. Our findings demonstrate the functional insight gained by integrating structural modeling and systematic literature curation, even for widely studied microorganisms. Functional annotations and protein structure models are available at https://tuberculosis.sdsu.edu/H37Rv in human- and machine-readable formats. IMPORTANCEMycobacterium tuberculosis, the primary causative agent of tuberculosis, kills more humans than any other infectious bacterium. Yet 40% of its genome is functionally uncharacterized, leaving much about the genetic basis of its resistance to antibiotics, capacity to withstand host immunity, and basic metabolism yet undiscovered. Irregular literature curation for functional annotation contributes to this gap. We systematically curated functions from literature and structural similarity for over half of poorly characterized genes, expanding the functionally annotated Mycobacterium tuberculosis proteome. Applying this updated annotation to recent in vivo functional screens added functional information to dozens of clinically pertinent proteins described as having unknown function. Integrating the annotations with a prospective functional screen identified new mutants resistant to a first-line TB drug, supporting an emerging hypothesis for its mode of action. These improvements in functional interpretation of clinically informative studies underscore the translational value of this functional knowledge. Structure-derived annotations identify hundreds of high-confidence candidates for mechanisms of antibiotic resistance, virulence factors, and basic metabolism and other functions key in clinical and basic tuberculosis research. More broadly, they provide a systematic framework for improving prokaryotic reference annotations.
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7
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Zabelkin A, Yakovleva Y, Bochkareva O, Alexeev N. PaReBrick: PArallel REarrangements and BReaks identification toolkit. Bioinformatics 2021; 38:357-363. [PMID: 34601581 PMCID: PMC8723149 DOI: 10.1093/bioinformatics/btab691] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/25/2021] [Accepted: 09/29/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION High plasticity of bacterial genomes is provided by numerous mechanisms including horizontal gene transfer and recombination via numerous flanking repeats. Genome rearrangements such as inversions, deletions, insertions and duplications may independently occur in different strains, providing parallel adaptation or phenotypic diversity. Specifically, such rearrangements might be responsible for virulence, antibiotic resistance and antigenic variation. However, identification of such events requires laborious manual inspection and verification of phyletic pattern consistency. RESULTS Here, we define the term 'parallel rearrangements' as events that occur independently in phylogenetically distant bacterial strains and present a formalization of the problem of parallel rearrangements calling. We implement an algorithmic solution for the identification of parallel rearrangements in bacterial populations as a tool PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their parallelism score. The tool provides diagrams of the neighbors for each block of interest, allowing the detection of horizontally transferred blocks or their extra copies and the inversions in which copied blocks are involved. We demonstrated PaReBrick's efficiency and accuracy and showed its potential to detect genome rearrangements responsible for pathogenicity and adaptation in bacterial genomes. AVAILABILITY AND IMPLEMENTATION PaReBrick is written in Python and is available on GitHub: https://github.com/ctlab/parallel-rearrangements. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Alexey Zabelkin
- Computer Technologies Laboratory, ITMO University, St Petersburg 197101, Russia
- Bioinformatics Institute, St Petersburg 194100, Russia
| | - Yulia Yakovleva
- Bioinformatics Institute, St Petersburg 194100, Russia
- Department of Microbiology, Faculty of Biology, Saint Petersburg State University, St Petersburg 199034, Russia
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8
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Repar J, Zahradka D, Sović I, Zahradka K. Characterization of gross genome rearrangements in Deinococcus radiodurans recA mutants. Sci Rep 2021; 11:10939. [PMID: 34035321 PMCID: PMC8149714 DOI: 10.1038/s41598-021-89173-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/21/2021] [Indexed: 02/04/2023] Open
Abstract
Genome stability in radioresistant bacterium Deinococcus radiodurans depends on RecA, the main bacterial recombinase. Without RecA, gross genome rearrangements occur during repair of DNA double-strand breaks. Long repeated (insertion) sequences have been identified as hot spots for ectopic recombination leading to genome rearrangements, and single-strand annealing (SSA) postulated to be the most likely mechanism involved in this process. Here, we have sequenced five isolates of D. radiodurans recA mutant carrying gross genome rearrangements to precisely characterize the rearrangements and to elucidate the underlying repair mechanism. The detected rearrangements consisted of large deletions in chromosome II in all the sequenced recA isolates. The mechanism behind these deletions clearly differs from the classical SSA; it utilized short (4-11 bp) repeats as opposed to insertion sequences or other long repeats. Moreover, it worked over larger linear DNA distances from those previously tested. Our data are most compatible with alternative end-joining, a recombination mechanism that operates in eukaryotes, but is also found in Escherichia coli. Additionally, despite the recA isolates being preselected for different rearrangement patterns, all identified deletions were found to overlap in a 35 kb genomic region. We weigh the evidence for mechanistic vs. adaptive reasons for this phenomenon.
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Affiliation(s)
- Jelena Repar
- grid.4905.80000 0004 0635 7705Laboratory for Molecular Microbiology, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Davor Zahradka
- grid.4905.80000 0004 0635 7705Laboratory for Molecular Microbiology, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ivan Sović
- Digital BioLogic d.o.o, Ivanić-Grad, Croatia
| | - Ksenija Zahradka
- grid.4905.80000 0004 0635 7705Laboratory for Molecular Microbiology, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
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9
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Liu T, Luo H, Gao F. Position preference of essential genes in prokaryotic operons. PLoS One 2021; 16:e0250380. [PMID: 33886641 PMCID: PMC8061932 DOI: 10.1371/journal.pone.0250380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 04/05/2021] [Indexed: 11/19/2022] Open
Abstract
Essential genes, which form the basis of life activities, are crucial for the survival of organisms. Essential genes tend to be located in operons, but how they are distributed in operons is still unclear for most prokaryotes. In order to clarify the general rule of position preference of essential genes in operons, an index of the average position of genes in an operon was proposed, and the distributions of essential and non-essential genes in operons in 51 bacterial genomes and two archaeal genomes were analyzed based on this new index. Consequently, essential genes were found to preferentially occupy the front positions of the operons, which tend to be expressed at higher levels.
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Affiliation(s)
- Tao Liu
- Department of Physics, School of Science, Tianjin University, Tianjin, China
| | - Hao Luo
- Department of Physics, School of Science, Tianjin University, Tianjin, China
- * E-mail: (FG); (HL)
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
- * E-mail: (FG); (HL)
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10
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Abdel-Glil MY, Thomas P, Linde J, Busch A, Wieler LH, Neubauer H, Seyboldt C. Comparative in silico genome analysis of Clostridium perfringens unravels stable phylogroups with different genome characteristics and pathogenic potential. Sci Rep 2021; 11:6756. [PMID: 33762628 PMCID: PMC7991664 DOI: 10.1038/s41598-021-86148-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 03/11/2021] [Indexed: 12/16/2022] Open
Abstract
Clostridium perfringens causes a plethora of devastating infections, with toxin production being the underlying mechanism of pathogenicity in various hosts. Genomic analyses of 206 public-available C. perfringens strains´ sequence data identified a substantial degree of genomic variability in respect to episome content, chromosome size and mobile elements. However, the position and order of the local collinear blocks on the chromosome showed a considerable degree of preservation. The strains were divided into five stable phylogroups (I–V). Phylogroup I contained human food poisoning strains with chromosomal enterotoxin (cpe) and a Darmbrand strain characterized by a high frequency of mobile elements, a relatively small genome size and a marked loss of chromosomal genes, including loss of genes encoding virulence traits. These features might correspond to the adaptation of these strains to a particular habitat, causing human foodborne illnesses. This contrasts strains that belong to phylogroup II where the genome size points to the acquisition of genetic material. Most strains of phylogroup II have been isolated from enteric lesions in horses and dogs. Phylogroups III, IV and V are heterogeneous groups containing a variety of different strains, with phylogroup III being the most abundant (65.5%). In conclusion, C. perfringens displays five stable phylogroups reflecting different disease involvements, prompting further studies on the evolution of this highly important pathogen.
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Affiliation(s)
- Mostafa Y Abdel-Glil
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96A, 07743, Jena, Germany. .,Department of Pathology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia Province, Egypt.
| | - Prasad Thomas
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96A, 07743, Jena, Germany.,Division of Bacteriology and Mycology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, India
| | - Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96A, 07743, Jena, Germany
| | - Anne Busch
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96A, 07743, Jena, Germany.,Department of Anaesthesiology and Intensive Care Medicine, University Hospital Jena, Am Klinikum 1, 07747, Jena, Germany
| | - Lothar H Wieler
- Robert Koch-Institut, Nordufer 20, 13353, Berlin, Germany.,Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universität, Robert-von-Ostertag-Str. 7-13, Building 35, 14163, Berlin, Germany
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96A, 07743, Jena, Germany
| | - Christian Seyboldt
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96A, 07743, Jena, Germany.
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Top J, Arredondo-Alonso S, Schürch AC, Puranen S, Pesonen M, Pensar J, Willems RJL, Corander J. Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen, Enterococcus faecium. Microb Genom 2020; 6:mgen000488. [PMID: 33253085 PMCID: PMC8116687 DOI: 10.1099/mgen.0.000488] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 11/16/2020] [Indexed: 11/25/2022] Open
Abstract
Enterococcus faecium is a gut commensal of the gastro-digestive tract, but also known as nosocomial pathogen among hospitalized patients. Population genetics based on whole-genome sequencing has revealed that E. faecium strains from hospitalized patients form a distinct clade, designated clade A1, and that plasmids are major contributors to the emergence of nosocomial E. faecium. Here we further explored the adaptive evolution of E. faecium using a genome-wide co-evolution study (GWES) to identify co-evolving single-nucleotide polymorphisms (SNPs). We identified three genomic regions harbouring large numbers of SNPs in tight linkage that are not proximal to each other based on the completely assembled chromosome of the clade A1 reference hospital isolate AUS0004. Close examination of these regions revealed that they are located at the borders of four different types of large-scale genomic rearrangements, insertion sites of two different genomic islands and an IS30-like transposon. In non-clade A1 isolates, these regions are adjacent to each other and they lack the insertions of the genomic islands and IS30-like transposon. Additionally, among the clade A1 isolates there is one group of pet isolates lacking the genomic rearrangement and insertion of the genomic islands, suggesting a distinct evolutionary trajectory. In silico analysis of the biological functions of the genes encoded in three regions revealed a common link to a stress response. This suggests that these rearrangements may reflect adaptation to the stringent conditions in the hospital environment, such as antibiotics and detergents, to which bacteria are exposed. In conclusion, to our knowledge, this is the first study using GWES to identify genomic rearrangements, suggesting that there is considerable untapped potential to unravel hidden evolutionary signals from population genomic data.
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Affiliation(s)
- Janetta Top
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sergio Arredondo-Alonso
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Anita C. Schürch
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Santeri Puranen
- Department of Computer Science, Aalto University, FI-00076 Espoo, Finland
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology (HIIT), FI-00014 University of Helsinki, Finland
| | - Maiju Pesonen
- Department of Computer Science, Aalto University, FI-00076 Espoo, Finland
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology (HIIT), FI-00014 University of Helsinki, Finland
- Present address: Oslo Centre for Biostatistics and Epidemiology (OCBE), Oslo University Hospital Research Support Services, Oslo, Norway
| | - Johan Pensar
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology (HIIT), FI-00014 University of Helsinki, Finland
- Present address: Department of Mathematics, University of Oslo, 0316 Oslo, Norway
| | - Rob J. L. Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jukka Corander
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology (HIIT), FI-00014 University of Helsinki, Finland
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
- Department of Biostatistics, University of Oslo, 0317 Oslo, Norway
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Soler-Bistué A, Aguilar-Pierlé S, Garcia-Garcerá M, Val ME, Sismeiro O, Varet H, Sieira R, Krin E, Skovgaard O, Comerci DJ, Rocha EPC, Mazel D. Macromolecular crowding links ribosomal protein gene dosage to growth rate in Vibrio cholerae. BMC Biol 2020; 18:43. [PMID: 32349767 PMCID: PMC7191768 DOI: 10.1186/s12915-020-00777-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/31/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND In fast-growing bacteria, the genomic location of ribosomal protein (RP) genes is biased towards the replication origin (oriC). This trait allows optimizing their expression during exponential phase since oriC neighboring regions are in higher dose due to multifork replication. Relocation of s10-spc-α locus (S10), which codes for most of the RP, to ectopic genomic positions shows that its relative distance to the oriC correlates to a reduction on its dosage, its expression, and bacterial growth rate. However, a mechanism linking S10 dosage to cell physiology has still not been determined. RESULTS We hypothesized that S10 dosage perturbations impact protein synthesis capacity. Strikingly, we observed that in Vibrio cholerae, protein production capacity was independent of S10 position. Deep sequencing revealed that S10 relocation altered chromosomal replication dynamics and genome-wide transcription. Such changes increased as a function of oriC-S10 distance. Since RP constitutes a large proportion of cell mass, lower S10 dosage could lead to changes in macromolecular crowding, impacting cell physiology. Accordingly, cytoplasm fluidity was higher in mutants where S10 is most distant from oriC. In hyperosmotic conditions, when crowding differences are minimized, the growth rate and replication dynamics were highly alleviated in these strains. CONCLUSIONS The genomic location of RP genes ensures its optimal dosage. However, besides of its essential function in translation, their genomic position sustains an optimal macromolecular crowding essential for maximizing growth. Hence, this could be another mechanism coordinating DNA replication to bacterial growth.
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Affiliation(s)
- Alfonso Soler-Bistué
- Institut Pasteur, Unité Plasticité du Génome Bactérien, UMR3525, CNRS, Paris, France
- Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo A. Ugalde," CONICET - Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | | | - Marc Garcia-Garcerá
- Microbial Evolutionary Genomics, Département Génomes et Génétique, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique UMR3525, Paris, France
- Department of Fundamental Microbiology, University of Lausanne, Quartier SORGE, 1003, Lausanne, Switzerland
| | - Marie-Eve Val
- Institut Pasteur, Unité Plasticité du Génome Bactérien, UMR3525, CNRS, Paris, France
| | - Odile Sismeiro
- Institut Pasteur, Plate-forme Transcriptome et Épigenome, Biomics, Centre d'Innovation et Recherche Technologique (Citech), Paris, France
| | - Hugo Varet
- Institut Pasteur, Plate-forme Transcriptome et Épigenome, Biomics, Centre d'Innovation et Recherche Technologique (Citech), Paris, France
| | - Rodrigo Sieira
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - Evelyne Krin
- Institut Pasteur, Unité Plasticité du Génome Bactérien, UMR3525, CNRS, Paris, France
| | - Ole Skovgaard
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Diego J Comerci
- Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo A. Ugalde," CONICET - Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Département Génomes et Génétique, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique UMR3525, Paris, France
| | - Didier Mazel
- Institut Pasteur, Unité Plasticité du Génome Bactérien, UMR3525, CNRS, Paris, France.
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Alexandraki V, Kazou M, Blom J, Pot B, Papadimitriou K, Tsakalidou E. Comparative Genomics of Streptococcus thermophilus Support Important Traits Concerning the Evolution, Biology and Technological Properties of the Species. Front Microbiol 2019; 10:2916. [PMID: 31956321 PMCID: PMC6951406 DOI: 10.3389/fmicb.2019.02916] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 12/03/2019] [Indexed: 12/24/2022] Open
Abstract
Streptococcus thermophilus is a major starter for the dairy industry with great economic importance. In this study we analyzed 23 fully sequenced genomes of S. thermophilus to highlight novel aspects of the evolution, biology and technological properties of this species. Pan/core genome analysis revealed that the species has an important number of conserved genes and that the pan genome is probably going to be closed soon. According to whole genome phylogeny and average nucleotide identity (ANI) analysis, most S. thermophilus strains were grouped in two major clusters (i.e., clusters A and B). More specifically, cluster A includes strains with chromosomes above 1.83 Mbp, while cluster B includes chromosomes below this threshold. This observation suggests that strains belonging to the two clusters may be differentiated by gene gain or gene loss events. Furthermore, certain strains of cluster A could be further subdivided in subgroups, i.e., subgroup I (ASCC 1275, DGCC 7710, KLDS SM, MN-BM-A02, and ND07), II (MN-BM-A01 and MN-ZLW-002), III (LMD-9 and SMQ-301), and IV (APC151 and ND03). In cluster B certain strains formed one distinct subgroup, i.e., subgroup I (CNRZ1066, CS8, EPS, and S9). Clusters and subgroups observed for S. thermophilus indicate the existence of lineages within the species, an observation which was further supported to a variable degree by the distribution and/or the architecture of several genomic traits. These would include exopolysaccharide (EPS) gene clusters, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)-CRISPR associated (Cas) systems, as well as restriction-modification (R-M) systems and genomic islands (GIs). Of note, the histidine biosynthetic cluster was found present in all cluster A strains (plus strain NCTC12958T) but was absent from all strains in cluster B. Other loci related to lactose/galactose catabolism and urea metabolism, aminopeptidases, the majority of amino acid and peptide transporters, as well as amino acid biosynthetic pathways were found to be conserved in all strains suggesting their central role for the species. Our study highlights the necessity of sequencing and analyzing more S. thermophilus complete genomes to further elucidate important aspects of strain diversity within this starter culture that may be related to its application in the dairy industry.
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Affiliation(s)
- Voula Alexandraki
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Maria Kazou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Bruno Pot
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Department of Bioengineering Sciences (DBIT), Vrije Universiteit Brussel, Brussels, Belgium
| | - Konstantinos Papadimitriou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Effie Tsakalidou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
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14
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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: 8] [Impact Index Per Article: 1.6] [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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15
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Bochkareva OO, Moroz EV, Davydov II, Gelfand MS. Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics 2018; 19:965. [PMID: 30587126 PMCID: PMC6307245 DOI: 10.1186/s12864-018-5245-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 11/14/2018] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization, generally comprised of 2-3 chromosomes. RESULTS We performed integrated genomic analysis of 127 Burkholderia strains. The pan-genome is open with the saturation to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements indicate a strong avoidance of intra-replichore inversions that is likely caused by selection against the transfer of large groups of genes between the leading and the lagging strands. Translocated genes also tend to retain their position in the leading or the lagging strand, and this selection is stronger for large syntenies. Integrated reconstruction of chromosome rearrangements in the context of strains phylogeny reveals parallel rearrangements that may indicate inversion-based phase variation and integration of new genomic islands. In particular, we detected parallel inversions in the second chromosomes of B. pseudomallei with breakpoints formed by genes encoding membrane components of multidrug resistance complex, that may be linked to a phase variation mechanism. Two genomic islands, spreading horizontally between chromosomes, were detected in the B. cepacia group. CONCLUSIONS This study demonstrates the power of integrated analysis of pan-genomes, chromosome rearrangements, and selection regimes. Non-random inversion patterns indicate selective pressure, inversions are particularly frequent in a recent pathogen B. mallei, and, together with periods of positive selection at other branches, may indicate adaptation to new niches. One such adaptation could be a possible phase variation mechanism in B. pseudomallei.
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Affiliation(s)
- Olga O. Bochkareva
- Kharkevich Institute for Information Transmission Problems, Moscow, Russia
- Center of Life Sciences Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Elena V. Moroz
- Kharkevich Institute for Information Transmission Problems, Moscow, Russia
| | - Iakov I. Davydov
- Department of Ecology and Evolution & Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Mikhail S. Gelfand
- Kharkevich Institute for Information Transmission Problems, Moscow, 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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Ausiannikava D, Mitchell L, Marriott H, Smith V, Hawkins M, Makarova KS, Koonin EV, Nieduszynski CA, Allers T. Evolution of Genome Architecture in Archaea: Spontaneous Generation of a New Chromosome in Haloferax volcanii. Mol Biol Evol 2018; 35:1855-1868. [PMID: 29668953 PMCID: PMC6063281 DOI: 10.1093/molbev/msy075] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The common ancestry of archaea and eukaryotes is evident in their genome architecture. All eukaryotic and several archaeal genomes consist of multiple chromosomes, each replicated from multiple origins. Three scenarios have been proposed for the evolution of this genome architecture: 1) mutational diversification of a multi-copy chromosome; 2) capture of a new chromosome by horizontal transfer; 3) acquisition of new origins and splitting into two replication-competent chromosomes. We report an example of the third scenario: the multi-origin chromosome of the archaeon Haloferax volcanii has split into two elements via homologous recombination. The newly generated elements are bona fide chromosomes, because each bears "chromosomal" replication origins, rRNA loci, and essential genes. The new chromosomes were stable during routine growth but additional genetic manipulation, which involves selective bottlenecks, provoked further rearrangements. To the best of our knowledge, rearrangement of a naturally evolved prokaryotic genome to generate two new chromosomes has not been described previously.
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Affiliation(s)
- Darya Ausiannikava
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Laura Mitchell
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Hannah Marriott
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Victoria Smith
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Michelle Hawkins
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD
| | | | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
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17
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Hendrickson HL, Barbeau D, Ceschin R, Lawrence JG. Chromosome architecture constrains horizontal gene transfer in bacteria. PLoS Genet 2018; 14:e1007421. [PMID: 29813058 PMCID: PMC5993296 DOI: 10.1371/journal.pgen.1007421] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 06/08/2018] [Accepted: 05/16/2018] [Indexed: 11/19/2022] Open
Abstract
Despite significant frequencies of lateral gene transfer between species, higher taxonomic groups of bacteria show ecological and phenotypic cohesion. This suggests that barriers prevent panmictic dissemination of genes via lateral gene transfer. We have proposed that most bacterial genomes have a functional architecture imposed by Architecture IMparting Sequences (AIMS). AIMS are defined as 8 base pair sequences preferentially abundant on leading strands, whose abundance and strand-bias are positively correlated with proximity to the replication terminus. We determined that inversions whose endpoints lie within a single chromosome arm, which would reverse the polarity of AIMS in the inverted region, are both shorter and less frequent near the replication terminus. This distribution is consistent with the increased selection on AIMS function in this region, thus constraining DNA rearrangement. To test the hypothesis that AIMS also constrain DNA transfer between genomes, AIMS were identified in genomes while ignoring atypical, potentially laterally-transferred genes. The strand-bias of AIMS within recently acquired genes was negatively correlated with the distance of those genes from their genome’s replication terminus. This suggests that selection for AIMS function prevents the acquisition of genes whose AIMS are not found predominantly in the permissive orientation. This constraint has led to the loss of at least 18% of genes acquired by transfer in the terminus-proximal region. We used completely sequenced genomes to produce a predictive road map of paths of expected horizontal gene transfer between species based on AIMS compatibility between donor and recipient genomes. These results support a model whereby organisms retain introgressed genes only if the benefits conferred by their encoded functions outweigh the detriments incurred by the presence of foreign DNA lacking genome-wide architectural information. The potential success of horizontal gene transfer events is historically equated to the benefits conferred by encoded products. Here we show that gene transfer events are observed less frequently if the introduced genes disrupt important patterns of genomic information, suggesting that this disruption would confer an unacceptable cost. As a result, gene transfer events are less likely to be successful if the potential donor genomes have incompatible genome architecture. Because more distantly-related genes are less compatible, chromosome architecture serves as a mechanism to bias gene transfer events to those involving closer relatives, thereby providing a mechanism for the genotypic and phenotypic cohesion of higher taxonomic groups.
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Affiliation(s)
- Heather L. Hendrickson
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Dominique Barbeau
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Robin Ceschin
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jeffrey G. Lawrence
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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