Comparative genomics unravels mechanisms of genetic adaptation for the catabolism of the phenylurea herbicide linuron in Variovorax

AbstractBiodegradation of the phenylurea herbicide linuron appears a specialization within a specific clade of the Variovorax genus. The linuron catabolic ability is likely acquired by horizontal gene transfer but the mechanisms involved are not known. The full genome sequences of six linuron degrading Variovorax strains isolated from geographically distant locations were analyzed to acquire insight in the mechanisms of genetic adaptation towards linuron metabolism in Variovorax. Whole genome sequence analysis confirmed the phylogenetic position of the linuron degraders in a separate clade within Variovorax and indicated their unlikely origin from a common ancestral linuron degrader. The linuron degraders differentiated from non-degraders by the presence of multiple plasmids of 20 to 839 kb, including plasmids of unknown plasmid groups. The linuron catabolic gene clusters showed (i) high conservation and synteny and (ii) strain-dependent distribution among the different plasmids. All were bordered by IS1071 elements forming composite transposon structures appointing IS1071 as key for catabolic gene recruitment. Most of the strain carried at least one broad host range plasmid that might have been a second instrument for catabolic gene acquisition. We conclude that clade 1Variovorax strains, despite their different geographical origin, made use of a limited genetic repertoire to acquire linuron biodegradation.ImportanceThe genus Variovorax and especially a clade of strains that phylogenetically separates from the majority of Variovorax species, appears to be a specialist in the biodegradation of the phenyl urea herbicide linuron. Horizontal gene transfer (HGT) likely played an essential role in the genetic adaptation of those strain to acquire the linuron catabolic genotype. However, we do not know the genetic repertoire involved in this adaptation both regarding catabolic gene functions as well as gene functions that promote HGT neither do we know how this varies between the different strains. These questions are addressed in this paper by analyzing the full genome sequences of six linuron degrading Variovorax strains. This knowledge is important for understanding the mechanisms that steer world-wide genetic adaptation in a particular species and this for a particular phenotypic trait as linuron biodegradation.

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Comparative Genomics Suggests Mechanisms of Genetic Adaptation toward the Catabolism of the Phenylurea Herbicide Linuron in Variovorax

Genome Biology and Evolution ◽

10.1093/gbe/evaa085 ◽

2020 ◽

Vol 12 (6) ◽

pp. 827-841 ◽

Cited By ~ 3

Author(s):

Başak Öztürk ◽

Johannes Werner ◽

Jan P Meier-Kolthoff ◽

Boyke Bunk ◽

Cathrin Spröer ◽

...

Keyword(s):

Gene Clusters ◽

Whole Genome Sequence ◽

Phylogenetic Position ◽

Broad Host Range ◽

Genetic Adaptation ◽

Catabolic Gene ◽

Array Configuration ◽

Phenylurea Herbicide ◽

Catabolic Genes ◽

Clade 1

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Bacteriophage ϕMAM1, a Viunalikevirus, Is a Broad-Host-Range, High-Efficiency Generalized Transducer That Infects Environmental and Clinical Isolates of the Enterobacterial Genera Serratia and Kluyvera

Applied and Environmental Microbiology ◽

10.1128/aem.01546-14 ◽

2014 ◽

Vol 80 (20) ◽

pp. 6446-6457 ◽

Cited By ~ 22

Author(s):

Miguel A. Matilla ◽

George P. C. Salmond

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

High Efficiency ◽

Phylogenetic Analyses ◽

Clinical Isolates ◽

Host Recognition ◽

Broad Host Range ◽

Human Pathogens ◽

Serratia Plymuthica ◽

Content Type

ABSTRACTMembers of the enterobacterial genusSerratiaare ecologically widespread, and some strains are opportunistic human pathogens. Bacteriophage ϕMAM1 was isolated onSerratia plymuthicaA153, a biocontrol rhizosphere strain that produces the potently bioactive antifungal and anticancer haterumalide oocydin A. The ϕMAM1 phage is a generalized transducing phage that infects multiple environmental and clinical isolates ofSerratiaspp. and a rhizosphere strain ofKluyvera cryocrescens. Electron microscopy allowed classification of ϕMAM1 in the familyMyoviridae. Bacteriophage ϕMAM1 is virulent, uses capsular polysaccharides as a receptor, and can transduce chromosomal markers at frequencies of up to 7 × 10−6transductants per PFU. We also demonstrated transduction of the complete 77-kb oocydin A gene cluster and heterogeneric transduction of a plasmid carrying a type III toxin-antitoxin system. These results support the notion of the potential ecological importance of transducing phages in the acquisition of genes by horizontal gene transfer. Phylogenetic analyses grouped ϕMAM1 within the ViI-like bacteriophages, and genomic analyses revealed that the major differences between ϕMAM1 and other ViI-like phages arise in a region encoding the host recognition determinants. Our results predict that the wider genus of ViI-like phages could be efficient transducing phages, and this possibility has obvious implications for the ecology of horizontal gene transfer, bacterial functional genomics, and synthetic biology.

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Whole Genome Sequence Analysis of SARS-CoV-2 Strains Circulating in Malaysia During First Wave and Early Second Wave of Infections.

10.21203/rs.3.rs-81152/v1 ◽

2020 ◽

Author(s):

Zarina Mohd Zawawi ◽

Jeyanthi Suppiah ◽

Jeevanathan Kalyanasundram ◽

Muhammad Afif Azizan ◽

Shuhaila Mat-Sharani ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome Sequence ◽

Health Concern ◽

Whole Genome ◽

Sequencing Analysis ◽

Full Genome ◽

Sequencing Data ◽

Genome Sequences ◽

Synonymous Mutations

Abstract Background: Since December 2019, the outbreak of COVID-19 has raised a great public health concern globally. Here, we report the whole genome sequencing analysis of SARS-CoV-2 strains in Malaysia isolated from six patients diagnosed with COVID-19.Methods: The SARS-CoV-2 viral RNA extracted from clinical specimens and isolates were subjected to whole genome sequencing using NextSeq 500 platform. The sequencing data were assembled to full genome sequences using Megahit and phylogenetic tree was constructed using Mega X software.Results: Six full genome sequences of SARS-CoV-2 comprising of strains from 1st wave (25th January 2020) and 2nd wave (27th February 2020) infection were obtained. Downstream analysis demonstrated diversity among the Malaysian strains with several synonymous and non-synonymous mutations in four of the six cases, affecting the genes M, orf1ab, and S of the SARS-CoV-2 virus. The phylogenetic analysis revealed viral genome sequences of Malaysian SARS-CoV-2 strains clustered under the ancestral Type B.Conclusion: This study comprehended the SARS-CoV-2 virus evolution during its circulation in Malaysia. Continuous monitoring and analysis of the whole genome sequences of confirmed cases would be crucial to further understand the genetic evolution of the virus.

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Plasmids facilitate pathogenicity, not cooperation, in bacteria

10.21203/rs.3.rs-257679/v1 ◽

2021 ◽

Author(s):

Anna Dewar ◽

Joshua Thomas ◽

Thomas Scott ◽

Geoff Wild ◽

Ashleigh Griffin ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Pathogenic Bacteria ◽

Extracellular Proteins ◽

Gene Location ◽

Theoretical Modelling ◽

Broad Host Range ◽

Diverse Species ◽

Genomic Analyses ◽

Term Maintenance

Abstract Horizontal gene transfer via plasmids could favour cooperation in bacteria, because transfer of a cooperative gene turns non-cooperative cheats into cooperators. This hypothesis has received support from both theoretical and genomic analyses. In contrast, with a comparative analysis across 51 diverse species, we found that genes for extracellular proteins, which are likely to act as cooperative ‘public goods’, were not more likely to be carried on either: (i) plasmids compared to chromosomes; or (ii) plasmids that transfer at higher rates. Our results were supported by theoretical modelling which showed that while horizontal gene transfer can help cooperative genes initially invade a population, it does not favour the longer-term maintenance of cooperation. Instead, we found that genes for extracellular proteins were more likely to be on plasmids when they coded for pathogenic virulence traits, in pathogenic bacteria with a broad host-range. Taken together, these results support an alternate hypothesis, that plasmid gene location confers benefits other than horizontal gene transfer.

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UK circulating strains of human parainfluenza 3: an amplicon based next generation sequencing method and phylogenetic analysis

Wellcome Open Research ◽

10.12688/wellcomeopenres.14730.1 ◽

2018 ◽

Vol 3 ◽

pp. 118

Author(s):

Anna Smielewska ◽

Edward Emmott ◽

Kyriaki Ranellou ◽

Ashley Popay ◽

Ian Goodfellow ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Genome Sequence ◽

Sequence Data ◽

Hypervariable Region ◽

Whole Genome Sequence ◽

Whole Genome ◽

Full Genome ◽

Genome Sequences ◽

Genome Data ◽

The Uk

Background:Human parainfluenza viruses type 3 (HPIV3) are a prominent cause of respiratory infection with a significant impact in both pediatric and transplant patient cohorts. Currently there is a paucity of whole genome sequence data that would allow for detailed epidemiological and phylogenetic analysis of circulating strains in the UK. Although it is known that HPIV3 peaks annually in the UK, to date there are no whole genome sequences of HPIV3 UK strains available. Methods:Clinical strains were obtained from HPIV3 positive respiratory patient samples collected between 2011 and 2015. These were then amplified using an amplicon based method, sequenced on the Illumina platform and assembled using a new robust bioinformatics pipeline. Phylogenetic analysis was carried out in the context of other epidemiological studies and whole genome sequence data currently available with stringent exclusion of significantly culture-adapted strains of HPIV3.Results:In the current paper we have presented twenty full genome sequences of UK circulating strains of HPIV3 and a detailed phylogenetic analysis thereof. We have analysed the variability along the HPIV3 genome and identified a short hypervariable region in the non-coding segment between the M (matrix) and F (fusion) genes. The epidemiological classifications obtained by using this region and whole genome data were then compared and found to be identical.Conclusions:The majority of HPIV3 strains were observed at different geographical locations and with a wide temporal spread, reflecting the global distribution of HPIV3. Consistent with previous data, a particular subcluster or strain was not identified as specific to the UK, suggesting that a number of genetically diverse strains circulate at any one time. A small hypervariable region in the HPIV3 genome was identified and it was shown that, in the absence of full genome data, this region could be used for epidemiological surveillance of HPIV3.

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WHOLE GENOME COMPARISONS REVEALS A POSSIBLE CHIMERIC ORIGIN FOR A MAJOR METAZOAN ASSEMBLAGE

Journal of Biological System ◽

10.1142/s0218339010003408 ◽

2010 ◽

Vol 18 (02) ◽

pp. 261-275 ◽

Cited By ~ 6

Author(s):

MICHAEL SYVANEN ◽

JONATHAN DUCORE

Keyword(s):

Drosophila Melanogaster ◽

Caenorhabditis Elegans ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Sea Urchin ◽

Whole Genome ◽

Genome Sequences ◽

Phylogenetic Groups ◽

Molecular Studies ◽

Genome Comparisons

The availability of whole genome sequences from multiple metazoan phyla is making it possible to determine their phylogeny. We have found that a sea urchin and human define a clade that excludes a tunicate, contradicting both classical and recent molecular studies that place the tunicate and vertebrate in the Chordate phylum. Intriguingly, by means of a novel four taxa analysis, we have partitioned the 2000 proteins responsible for this assignment into two groups. One group, containing about 40% of the proteins, supports the classical assemblage of the tunicate with vertebrates, while the remaining group places the tunicate outside of the chordate assemblage. The existence of these two phylogenetic groups is robustly maintained in five, six and nine taxa analyses. These results suggest that major horizontal gene transfer events occurred during the emergence of one of the metazoan phyla. The simplest explanation is that the modern tunicate (as represented by Ciona intestinalis) began as a hybrid between a primitive vertebrate and some other organism, perhaps from an extinct and unidentified protostome phylum, at a time close to but after the diversification of the chordates and echinoderms and before the lineages leading to Drosophila melanogaster and Caenorhabditis elegans diverged.

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Frequent, independent transfers of a catabolic gene from bacteria to contrasted filamentous eukaryotes

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2014.0848 ◽

2014 ◽

Vol 281 (1789) ◽

pp. 20140848 ◽

Cited By ~ 27

Author(s):

Maxime Bruto ◽

Claire Prigent-Combaret ◽

Patricia Luis ◽

Yvan Moënne-Loccoz ◽

Daniel Muller

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Evolutionary History ◽

Eukaryotic Cells ◽

Phylogenomic Analysis ◽

Catabolic Gene ◽

Bacterial Phyla ◽

Bacterial Origin ◽

History Of ◽

Complex Evolutionary History

Even genetically distant prokaryotes can exchange genes between them, and these horizontal gene transfer events play a central role in adaptation and evolution. While this was long thought to be restricted to prokaryotes, certain eukaryotes have acquired genes of bacterial origin. However, gene acquisitions in eukaryotes are thought to be much less important in magnitude than in prokaryotes. Here, we describe the complex evolutionary history of a bacterial catabolic gene that has been transferred repeatedly from different bacterial phyla to stramenopiles and fungi. Indeed, phylogenomic analysis pointed to multiple acquisitions of the gene in these filamentous eukaryotes—as many as 15 different events for 65 microeukaryotes. Furthermore, once transferred, this gene acquired introns and was found expressed in mRNA databases for most recipients. Our results show that effective inter-domain transfers and subsequent adaptation of a prokaryotic gene in eukaryotic cells can happen at an unprecedented magnitude.

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Genome-wide estimation of recombination, mutation and positive selection enlightens diversification drivers of Mycobacterium bovis

Scientific Reports ◽

10.1038/s41598-021-98226-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Ana C. Reis ◽

Mónica V. Cunha

Keyword(s):

Comparative Genomics ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Positive Selection ◽

Population Expansion ◽

Whole Genome Sequence ◽

General Notion ◽

Terrestrial Mammals ◽

Evolutionary Forces ◽

Recombination System

AbstractGenome sequencing has reinvigorated the infectious disease research field, shedding light on disease epidemiology, pathogenesis, host–pathogen interactions and also evolutionary processes exerted upon pathogens. Mycobacterium tuberculosis complex (MTBC), enclosing M. bovis as one of its animal-adapted members causing tuberculosis (TB) in terrestrial mammals, is a paradigmatic model of bacterial evolution. As other MTBC members, M. bovis is postulated as a strictly clonal, slowly evolving pathogen, with apparently no signs of recombination or horizontal gene transfer. In this work, we applied comparative genomics to a whole genome sequence (WGS) dataset composed by 70 M. bovis from different lineages (European and African) to gain insights into the evolutionary forces that shape genetic diversification in M. bovis. Three distinct approaches were used to estimate signs of recombination. Globally, a small number of recombinant events was identified and confirmed by two independent methods with solid support. Still, recombination reveals a weaker effect on M. bovis diversity compared with mutation (overall r/m = 0.037). The differential r/m average values obtained across the clonal complexes of M. bovis in our dataset are consistent with the general notion that the extent of recombination may vary widely among lineages assigned to the same taxonomical species. Based on this work, recombination in M. bovis cannot be excluded and should thus be a topic of further effort in future comparative genomics studies for which WGS of large datasets from different epidemiological scenarios across the world is crucial. A smaller M. bovis dataset (n = 42) from a multi-host TB endemic scenario was then subjected to additional analyses, with the identification of more than 1,800 sites wherein at least one strain showed a single nucleotide polymorphism (SNP). The majority (87.1%) was located in coding regions, with the global ratio of non-synonymous upon synonymous alterations (dN/dS) exceeding 1.5, suggesting that positive selection is an important evolutionary force exerted upon M. bovis. A higher percentage of SNPs was detected in genes enriched into “lipid metabolism”, “cell wall and cell processes” and “intermediary metabolism and respiration” functional categories, revealing their underlying importance in M. bovis biology and evolution. A closer look on genes prone to horizontal gene transfer in the MTBC ancestor and included in the 3R (DNA repair, replication and recombination) system revealed a global average negative value for Taijima’s D neutrality test, suggesting that past selective sweeps and population expansion after a recent bottleneck remain as major evolutionary drivers of the obligatory pathogen M. bovis in its struggle with the host.

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The Phylogenomics of CRISPR-Cas System in Salmonella: an evolutionary race with housekeeping genes

10.1101/2020.07.08.193417 ◽

2020 ◽

Author(s):

Simran Krishnakant Kushwaha ◽

Chandrajit Lahiri ◽

Bahaa Abdella ◽

Sandhya Amol Marathe

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Virulence Factors ◽

Horizontal Gene Transfer Event ◽

Housekeeping Genes ◽

Broad Host Range ◽

Evolutionary Patterns ◽

Transfer Event ◽

Serovar Typhimurium ◽

Cas Genes

AbstractSalmonellae display intricate evolutionary patterns comprising over 2500 serovars having diverse pathogenic profiles. The acquisition/exchange of various virulence factors influence the evolutionary framework. To gain insights into evolution of Salmonella as a pathogen in association with the CRISPR-Cas genes we performed phylogenetic surveillance across strains of 22 Salmonella serovars. The strains assorted into two main clades, pertaining to the differences in their CRISPR1-leader and cas operon. Considering Salmonella enterica subsp. enterica serovar Typhimurium and serovar Typhi as signature serovars, we classified the clades as CRISPR1-STM/cas-STM and CRISPR1-STY/cas-STY, respectively. Serovars of the two clades displayed better relatedness, concerning CRISPR-1 leader and cas operon, across genera than between themselves. This signifies the acquisition of CRISPR1/Cas region a horizontal gene transfer event owing to the presence of mobile genetic elements flanking CRISPR1 array. The CRISPR2 tree does not show such relation. Spacer mapping of the two CRISPR arrays suggests the construct to be canonical, with only 8.8% spacer conservation among the serovars. As opposed to broad-host-range serovars, the host-specific serovars harbor fewer spacers. All typhoidal serovars have CRISPR1-STY/cas-STY system. Comparison of CRISPR and cas phenograms with that of multilocus sequence typing (MLST) suggests differential evolution of CRISPR/Cas system implying supplementary roles beyond immunity.

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Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance

10.1101/2021.12.08.471225 ◽

2021 ◽

Author(s):

Rauf Salamzade ◽

Abigail L. Manson ◽

Bruce J. Walker ◽

Thea Brennan-Krohn ◽

Colin J. Worby ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Genome Rearrangement ◽

Carbapenem Resistance ◽

Resistance Mechanisms ◽

Hospital Environment ◽

Whole Genome Sequence ◽

Diverse Range ◽

Carbapenem Resistant ◽

Genome Assemblies

Background: Carbapenem-resistant Enterobacterales (CRE) are an urgent global health threat. Inferring the dynamics of local CRE dissemination is currently limited by our inability to confidently trace the spread of resistance determinants to unrelated bacterial hosts. Whole genome sequence comparison is useful for identifying CRE clonal transmission and outbreaks, but high-frequency horizontal gene transfer (HGT) of carbapenem resistance genes and subsequent genome rearrangement complicate tracing the local persistence and mobilization of these genes across organisms. Methods: To overcome this limitation, we developed a new approach to identify recent HGT of large, near identical plasmid segments across species boundaries, which also allowed us to overcome technical challenges with genome assembly. We applied this to complete and near-complete genome assemblies to examine the local spread of CRE in a systematic, prospective collection of all CRE, as well as time- and species-matched carbapenem susceptible Enterobacterales, isolated from patients from four U.S. hospitals over nearly five years. Results: Our CRE collection comprised a diverse range of species, lineages and carbapenem resistance mechanisms, many of which were encoded on a variety of promiscuous plasmid types. We found and quantified rearrangement, persistence, and repeated transfer of plasmid segments, including those harboring carbapenemases, between organisms over multiple years. Some plasmid segments were found to be strongly associated with specific locales, thus representing geographic signatures that make it possible to trace recent and localized HGT events. Functional analysis of these signatures revealed genes commonly found in plasmids of nosocomial pathogens, such as functions required for plasmid retention and spread, as well survival against a variety of antibiotic and antiseptics common to the hospital environment. Conclusions: Collectively, the framework we developed provides a clearer, high resolution picture of the epidemiology of antibiotic resistance importation, spread, and persistence in patients and healthcare networks.

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