scholarly journals Phylogenetic analyses suggest centipede venom arsenals were repeatedly stocked by horizontal gene transfer

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Eivind A. B. Undheim ◽  
Ronald A. Jenner
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Phylogenetic Analyses ◽  
Gene Families ◽  
Venom Gland ◽  
Bacterial Gene ◽  
Multiple Gene ◽  
Genomic Analyses ◽  
Endogenous Proteins ◽  
Animal Venoms

AbstractVenoms have evolved over a hundred times in animals. Venom toxins are thought to evolve mostly by recruitment of endogenous proteins with physiological functions. Here we report phylogenetic analyses of venom proteome-annotated venom gland transcriptome data, assisted by genomic analyses, to show that centipede venoms have recruited at least five gene families from bacterial and fungal donors, involving at least eight horizontal gene transfer events. These results establish centipedes as currently the only known animals with venoms used in predation and defence that contain multiple gene families derived from horizontal gene transfer. The results also provide the first evidence for the implication of horizontal gene transfer in the evolutionary origin of venom in an animal lineage. Three of the bacterial gene families encode virulence factors, suggesting that horizontal gene transfer can provide a fast track channel for the evolution of novelty by the exaptation of bacterial weapons into animal venoms.

scholarly journals Plasmids Related to the Symbiotic Nitrogen Fixation Are Not Only Cooperated Functionally but Also May Have Evolved over a Time Span in Family Rhizobiaceae

2020 ◽  
Vol 12 (11) ◽  
pp. 2002-2014
Author(s):  
Ling-Ling Yang ◽  
Zhao Jiang ◽  
Yan Li ◽  
En-Tao Wang ◽  
Xiao-Yang Zhi
Keyword(s):  
Nitrogen Fixation ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Symbiotic Nitrogen Fixation ◽  
Gene Families ◽  
Time Span ◽  
Soil Conditions ◽  
Gene Gain ◽  
Nitrogen Fixing ◽  
Pan Genome

Abstract Rhizobia are soil bacteria capable of forming symbiotic nitrogen-fixing nodules associated with leguminous plants. In fast-growing legume-nodulating rhizobia, such as the species in the family Rhizobiaceae, the symbiotic plasmid is the main genetic basis for nitrogen-fixing symbiosis, and is susceptible to horizontal gene transfer. To further understand the symbioses evolution in Rhizobiaceae, we analyzed the pan-genome of this family based on 92 genomes of type/reference strains and reconstructed its phylogeny using a phylogenomics approach. Intriguingly, although the genetic expansion that occurred in chromosomal regions was the main reason for the high proportion of low-frequency flexible gene families in the pan-genome, gene gain events associated with accessory plasmids introduced more genes into the genomes of nitrogen-fixing species. For symbiotic plasmids, although horizontal gene transfer frequently occurred, transfer may be impeded by, such as, the host’s physical isolation and soil conditions, even among phylogenetically close species. During coevolution with leguminous hosts, the plasmid system, including accessory and symbiotic plasmids, may have evolved over a time span, and provided rhizobial species with the ability to adapt to various environmental conditions and helped them achieve nitrogen fixation. These findings provide new insights into the phylogeny of Rhizobiaceae and advance our understanding of the evolution of symbiotic nitrogen fixation.

scholarly journals Horizontal gene transfer in Histophilus somni and its role in the evolution of pathogenic strain 2336, as determined by comparative genomic analyses

BMC Genomics ◽  
2011 ◽  
Vol 12 (1) ◽  
Author(s):  
Shivakumara Siddaramappa ◽  
Jean F Challacombe ◽  
Alison J Duncan ◽  
Allison F Gillaspy ◽  
Matthew Carson ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Pathogenic Strain ◽  
Comparative Genomic ◽  
Histophilus Somni ◽  
Genomic Analyses

scholarly journals Reconstructing the Phylogeny of Corynebacteriales while Accounting for Horizontal Gene Transfer

2020 ◽  
Vol 12 (4) ◽  
pp. 381-395
Author(s):  
Nilson Da Rocha Coimbra ◽  
Aristoteles Goes-Neto ◽  
Vasco Azevedo ◽  
Aïda Ouangraoua
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Phylogenetic Trees ◽  
Bacterial Species ◽  
Gene Tree ◽  
Gene Families ◽  
Common Mechanism ◽  
Species Trees ◽  
Bacterial Phylogeny ◽  
Homologous Genes

Abstract Horizontal gene transfer is a common mechanism in Bacteria that has contributed to the genomic content of existing organisms. Traditional methods for estimating bacterial phylogeny, however, assume only vertical inheritance in the evolution of homologous genes, which may result in errors in the estimated phylogenies. We present a new method for estimating bacterial phylogeny that accounts for the presence of genes acquired by horizontal gene transfer between genomes. The method identifies and corrects putative transferred genes in gene families, before applying a gene tree-based summary method to estimate bacterial species trees. The method was applied to estimate the phylogeny of the order Corynebacteriales, which is the largest clade in the phylum Actinobacteria. We report a collection of 14 phylogenetic trees on 360 Corynebacteriales genomes. All estimated trees display each genus as a monophyletic clade. The trees also display several relationships proposed by past studies, as well as new relevant relationships between and within the main genera of Corynebacteriales: Corynebacterium, Mycobacterium, Nocardia, Rhodococcus, and Gordonia. An implementation of the method in Python is available on GitHub at https://github.com/UdeS-CoBIUS/EXECT (last accessed April 2, 2020).

scholarly journals 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

2014 ◽  
Vol 80 (20) ◽  
pp. 6446-6457 ◽  
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.

scholarly journals Comparative Genomics of the Archaea (Euryarchaeota): Evolution of Conserved Protein Families, the Stable Core, and the Variable Shell

1999 ◽  
Vol 9 (7) ◽  
pp. 608-628 ◽  
Author(s):  
Kira S. Makarova ◽  
L. Aravind ◽  
Michael Y. Galperin ◽  
Nick V. Grishin ◽  
Roman L. Tatusov ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gene Families ◽  
Small Subset ◽  
Specific Gene ◽  
Genome Replication ◽  
Protein Families ◽  
Archaeal Protein ◽  
The Core ◽  
Stable Core

Comparative analysis of the protein sequences encoded in the four euryarchaeal species whose genomes have been sequenced completely (Methanococcus jannaschii, Methanobacterium thermoautotrophicum, Archaeoglobus fulgidus, andPyrococcus horikoshii) revealed 1326 orthologous sets, of which 543 are represented in all four species. The proteins that belong to these conserved euryarchaeal families comprise 31%–35% of the gene complement and may be considered the evolutionarily stable core of the archaeal genomes. The core gene set includes the great majority of genes coding for proteins involved in genome replication and expression, but only a relatively small subset of metabolic functions. For many gene families that are conserved in all euryarchaea, previously undetected orthologs in bacteria and eukaryotes were identified. A number of euryarchaeal synapomorphies (unique shared characters) were identified; these are protein families that possess sequence signatures or domain architectures that are conserved in all euryarchaea but are not found in bacteria or eukaryotes. In addition, euryarchaea-specific expansions of several protein and domain families were detected. In terms of their apparent phylogenetic affinities, the archaeal protein families split into bacterial and eukaryotic families. The majority of the proteins that have only eukaryotic orthologs or show the greatest similarity to their eukaryotic counterparts belong to the core set. The families of euryarchaeal genes that are conserved in only two or three species constitute a relatively mobile component of the genomes whose evolution should have involved multiple events of lineage-specific gene loss and horizontal gene transfer. Frequently these proteins have detectable orthologs only in bacteria or show the greatest similarity to the bacterial homologs, which might suggest a significant role of horizontal gene transfer from bacteria in the evolution of the euryarchaeota.

scholarly journals Complex Evolution of Light-Dependent Protochlorophyllide Oxidoreductases in Aerobic Anoxygenic Phototrophs: Origin, Phylogeny, and Function

2020 ◽  
Author(s):  
Olga Chernomor ◽  
Lena Peters ◽  
Judith Schneidewind ◽  
Anita Loeschcke ◽  
Esther Knieps-Grünhagen ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Phylogenetic Analyses ◽  
Oxygenic Photosynthesis ◽  
Protochlorophyllide Oxidoreductase ◽  
Transfer Event ◽  
Anoxygenic Phototrophs ◽  
And Function

Abstract Light-dependent protochlorophyllide oxidoreductase (LPOR) and dark-operative protochlorophyllide oxidoreductase are evolutionary and structurally distinct enzymes that are essential for the synthesis of (bacterio)chlorophyll, the primary pigment needed for both anoxygenic and oxygenic photosynthesis. In contrast to the long-held hypothesis that LPORs are only present in oxygenic phototrophs, we recently identified a functional LPOR in the aerobic anoxygenic phototrophic bacterium (AAPB) Dinoroseobacter shibae and attributed its presence to a single horizontal gene transfer event from cyanobacteria. Here, we provide evidence for the more widespread presence of genuine LPOR enzymes in AAPBs. An exhaustive bioinformatics search identified 36 putative LPORs outside of oxygenic phototrophic bacteria (cyanobacteria) with the majority being AAPBs. Using in vitro and in vivo assays, we show that the large majority of the tested AAPB enzymes are genuine LPORs. Solution structural analyses, performed for two of the AAPB LPORs, revealed a globally conserved structure when compared with a well-characterized cyanobacterial LPOR. Phylogenetic analyses suggest that LPORs were transferred not only from cyanobacteria but also subsequently between proteobacteria and from proteobacteria to Gemmatimonadetes. Our study thus provides another interesting example for the complex evolutionary processes that govern the evolution of bacteria, involving multiple horizontal gene transfer events that likely occurred at different time points and involved different donors.

scholarly journals Plasmids facilitate pathogenicity, not cooperation, in bacteria

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.

scholarly journals Horizontally transferred fungal carotenoid genes in the two-spotted spider mite Tetranychus urticae

2011 ◽  
Vol 8 (2) ◽  
pp. 253-257 ◽  
Author(s):  
Boran Altincicek ◽  
Jennifer L. Kovacs ◽  
Nicole M. Gerardo
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Tetranychus Urticae ◽  
Spider Mite ◽  
Phylogenetic Analyses ◽  
Carotenoid Biosynthesis ◽  
Organic Pigments ◽  
Carotenoid Genes ◽  
Two Spotted Spider Mite ◽  
Micro Organisms

Carotenoids are organic pigments commonly synthesized by plants, algae and some micro-organisms. Through absorption of light energy, carotenoids facilitate photosynthesis and provide protection against photo-oxidation. While it was presumed that all carotenoids in animals were sequestered from their diets, aphids were recently shown to harbour genomic copies of functional carotenoid biosynthesis genes that were acquired via horizontal gene transfer from fungi. Our search of available animal transcripts revealed the presence of two related genes in the two-spotted spider mite Tetranychus urticae . Phylogenetic analyses suggest that the T. urticae genes were transferred from fungi into the spider mite genome, probably in a similar manner as recently suggested for aphids. The genes are expressed in both green and red morphs, with red morphs exhibiting higher levels of gene expression. Additionally, there appear to be changes in the expression of these genes during diapause. As carotenoids are associated with diapause induction in these animals, our results add to recent findings highlighting the importance of eukaryotic horizontal gene transfer in the ecology and evolution of higher animals.

scholarly journals De Novo Gene Birth, Horizontal Gene Transfer, and Gene Duplication as Sources of New Gene Families Associated with the Origin of Symbiosis in Amanita

2020 ◽  
Vol 12 (11) ◽  
pp. 2168-2182
Author(s):  
Yen-Wen Wang ◽  
Jaqueline Hess ◽  
Jason C Slot ◽  
Anne Pringle
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gene Duplication ◽  
De Novo ◽  
Gene Families ◽  
Negative Regulator ◽  
Orphan Gene ◽  
Unique Gene ◽  
De Novo Gene ◽  
New Gene

Abstract By introducing novel capacities and functions, new genes and gene families may play a crucial role in ecological transitions. Mechanisms generating new gene families include de novo gene birth, horizontal gene transfer, and neofunctionalization following a duplication event. The ectomycorrhizal (ECM) symbiosis is a ubiquitous mutualism and the association has evolved repeatedly and independently many times among the fungi, but the evolutionary dynamics enabling its emergence remain elusive. We developed a phylogenetic workflow to first understand if gene families unique to ECM Amanita fungi and absent from closely related asymbiotic species are functionally relevant to the symbiosis, and then to systematically infer their origins. We identified 109 gene families unique to ECM Amanita species. Genes belonging to unique gene families are under strong purifying selection and are upregulated during symbiosis, compared with genes of conserved or orphan gene families. The origins of seven of the unique gene families are strongly supported as either de novo gene birth (two gene families), horizontal gene transfer (four), or gene duplication (one). An additional 34 families appear new because of their selective retention within symbiotic species. Among the 109 unique gene families, the most upregulated gene in symbiotic cultures encodes a 1-aminocyclopropane-1-carboxylate deaminase, an enzyme capable of downregulating the synthesis of the plant hormone ethylene, a common negative regulator of plant-microbial mutualisms.

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