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53 results for “Horizontal gene transfer”
Supplementary phylogenetic data for Manzano-Marín et. al. 2020 "Serial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids' di-symbiotic systems"
<p>Supplementary data for Manzano-Marín et. al. 2019 "Serial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids' di-symbiotic systems".</p> <p>The data set consists of four folders:</p> <p>1) "Buchnera_phylo”: PHYLIP-formatted file used for phylogenetic reconstruction of <em>Buchnera</em> and resulting tree in NEWICK format.</p> <p>2) "Erwinia_phylo”: PHYLIP-formatted file used for phylogenetic reconstruction of <em>Erwinia</em> and resulting tree in NEWICK format.</p> <p>3) "Hamiltonella_phylo”: FASTA-formatted nucleotide alignment files of each gene and NEXUS-formatted files used for Bayesian phylogenetic reconstruction of <em>Hamiltonella</em> symbionts.</p> <p>4) "HGT_genes": FASTA-formatted nucleotide alignment files of each horizontally transferred gene and non-horizontally transferred genes nupC, and <em>gpmA</em>. Also, NEXUS-formatted files used for Bayesian phylogenetic reconstruction and of resulting trees.</p> <p>5) "Tn3_pylo": FASTA-formatted amino acid alignment files of mobile elements related to the Tn3 family resolvase/invertase found in <em>Hamiltonella</em>-associated <em>Erwinia haradaeae</em> symbionts. Also, NEXUS-formatted files used for Bayesian phylogenetic reconstruction and of resulting trees.</p>
No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini
<p><strong>No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini</strong></p> <p>These files accompany the peer-reviewed version of http://dx.doi.org/10.1101/033464</p> <p>A previous dataset https://zenodo.org/record/45162 accompanied the version of this manuscript at BioRxiv - biorxiv.org/content/early/2015/12/13/033464</p> <p>This dataset includes all files from https://zenodo.org/record/45162 plus all the Supplemental files, and one additional file HGT_phylogenetic_files.tgz. All files are described in Hypsibius_dujardini_files_README.md</p> <p><strong>Abstract</strong></p> <p>Tardigrades are meiofaunal ecdysozoans that are key to understanding the origins of Arthropoda. Many species of Tardigrada can survive extreme conditions through cryptobiosis. In a recent paper (Boothby TC <em>et al </em>(2015) Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. <em>Proc Natl Acad Sci USA</em> 112:15976-15981) the authors concluded that the tardigrade <em>Hypsibius dujardini </em>had an unprecedented proportion (17%) of genes originating through functional horizontal gene transfer (fHGT), and speculated that fHGT was likely formative in the evolution of cryptobiosis. We independently sequenced the genome of <em>H. dujardini</em>. As expected from whole-organism DNA sampling, our raw data contained reads from non-target genomes. Filtering using metagenomics approaches generated a draft <em>H. dujardini</em> genome assembly of 135 Mb with superior assembly metrics to the previously published assembly. Additional microbial contamination likely remains. We found no support for extensive fHGT. Among 23,021 gene predictions we identified 0.2% strong candidates for fHGT from bacteria, and 0.2% strong candidates for fHGT from non-metazoan eukaryotes. Cross-comparison of assemblies showed that the overwhelming majority of HGT candidates in the Boothby <em>et al.</em> genome derived from contaminants. We conclude that fHGT into <em>H. dujardini </em>accounts for at most 1-2% of genes and that the proposal that one sixth of tardigrade genes originate from functional HGT events is an artefact of undetected contamination.</p> <p> </p>
Comparative genomics of eight aphid subfamilies reveals variable relationships between host horizontally-transferred genes and symbiont peptidoglycan metabolism.
<p>Genome assemblies, annotations, and orthologs of aphids (<em>Geopemphigus sp.</em>, <em>Stegophylla sp.</em>, <em>Chaitophorus viminalis</em>, and<em> Pemphigus obesinymphae</em>) and their symbionts. </p> <p>step1_final_assemblies_and_annotations.tar.gz: Aphid genomes and annotations</p> <p>step2_protein_evidence_used_for_genome_annotation.tar.gz: Protein evidence used for aphid genome annotation</p> <p>step3_amino_acid_inputs_for_aphid_orthologs: amino acid inputs for aphid ortholog assignmentt</p> <p>step5_buchnera_genomes_and_annotations.tar.gz: Buchnera genomes and annotations</p>
Data from: Comparative genomics reveals high rates of horizontal transfer and strong purifying selection on rhizobial symbiosis genes
<p class="western"><span>Horizontal transfer (HT) alters the repertoire of symbiosis genes in rhizobial genomes and may play an important role in the on-going evolution of the rhizobia-legume symbiosis. To gain insight into the extent of HT of symbiosis genes with different functional roles (nodulation, N-fixation, host benefit, and symbiont fitness), we conducted comparative genomic and selection analyses of the full genome sequences from 27 rhizobial genomes. We find that symbiosis genes experience high rates of HT among rhizobial lineages but also bear signatures of purifying selection (low Ka:Ks). HT and purifying selection appear to be particularly strong in genes involved in initiating the symbiosis (e.g. nodulation) and in genome-wide association candidates for mediating variation in benefits provided to the host. These patterns are consistent with rhizobia adapting to the host environment through the loss and gain of symbiosis genes, but not with host-imposed positive selection driving divergence of symbiosis genes through recurring bouts of positive selection.</span></p>
Processed data for Evidence of horizontal gene transfer and environmental selection impacting antibiotic resistance evolution in soil-dwelling Listeria
<p>Processed/source data for the manuscript Evidence of horizontal gene transfer and environmental selection impacting antibiotic resistance evolution in soil-dwelling <em>Listeria</em>.</p>
Dataset from: The origin and fate of fungal mitochondrial horizontal gene transferred sequences in orchids (Orchidaceae)
<p>The transfer of DNA among distantly related organisms is relatively common in bacteria but less prevalent in eukaryotes. Among fungi and plants, few of these events have been reported. Two segments of fungal mitochondrial DNA have been discovered in the mitogenome of orchids. Here, we build on their work to understand the timing of those transfer events, which orchids retain the fungal DNA, and the fate of the foreign DNA during orchid evolution. We update the content of the large DNA fragment and establish that it was transferred to the most recent common ancestor of a highly diverse clade of epidendroid orchids that lived ~28–43 Mya. Also, we present hypotheses of the origin of the small transferred fragment. Our findings deepen the knowledge of these interesting DNA transfers among organelles and we formulate a probable mechanism for these horizontal gene transfer events.</p>
Data from: Comparative genomics reveals high rates of horizontal transfer and strong purifying selection on rhizobial symbiosis genes
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Dataset from: The origin and fate of fungal mitochondrial horizontal gene transferred sequences in orchids (Orchidaceae)
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Data from: Experimental horizontal transfer of phage-derived genes to Drosophila confers innate immunity to parasitoids
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Data from: De novo gene birth, horizontal gene transfer and gene duplication as sources of new gene families associated with the origin of a symbiosis in Amanita
<p>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 <i>de novo</i> 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 molecular dynamics enabling its emergence remain elusive. We developed a phylogenetic workflow to first understand if gene families unique to ECM <i>Amanita</i> 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 <i>Amanita </i>species. Genes belonging to unique gene families are under strong purifying selection and are upregulated during symbiosis, compared to genes of conserved or orphan gene families. The origins of seven of the unique gene families are strongly supported as either <i>de novo</i> gene birth (two gene families), horizontal gene transfer (four), and 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 an ACC deaminase, an enzyme capable of downregulating the synthesis of the plant hormone ethylene. Ethylene is a common negative regulator of plant-microbial mutualisms.</p>
Data from: Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis
The opportunistic pathogens Staphylococcus aureus and Staphylococcus epidermidis represent major causes of severe nosocomial infection, and are associated with high levels of mortality and morbidity worldwide. These species are both common commensals on the human skin and in the nasal pharynx, but are genetically distinct, differing at 24% average nucleotide divergence in 1,478 core genes. To better understand the genome dynamics of these ecologically similar staphylococcal species, we carried out a comparative analysis of 324 S. aureus and S. epidermidis genomes, including 83 novel S. epidermidis sequences. A reference pan-genome approach and whole genome multilocus-sequence typing revealed that around half of the genome was shared between the species. Based on a BratNextGen analysis, homologous recombination was found to have impacted on 40% of the core genes in S. epidermidis, but on only 24% of the core genes in S. aureus. Homologous recombination between the species is rare, with a maximum of nine gene alleles shared between any two S. epidermidis and S. aureus isolates. In contrast, there was considerable interspecies admixture of mobile elements, in particular genes associated with the SaPIn1 pathogenicity island, metal detoxification, and the methicillin-resistance island SCCmec. Our data and analysis provide a context for considering the nature of recombinational boundaries between S. aureus and S. epidermidis and, the selective forces that influence realized recombination between these species.
Data from: Sequential horizontal gene transfers from different hosts in a widespread Eurasian parasitic plant, Cynomorium coccineum
Premise of the study: Parasites with large geographic ranges, and different hosts in parts of their range, might acquire horizontally-transferred genes (HGTs), which might sometimes leave a footprint of gradual host and range expansion. Cynomorium coccineum, the only member of the Saxifragales family Cynomoriaceae, is a root holoparasite that occurs in water-stressed habitats from western China to the Canary Islands. It parasitizes at least ten angiosperm families from different orders, some of them only in parts of its range. This parasite therefore offers an opportunity to trace HGTs as long as parasite/host pairs can be obtained and sequenced. Methods: By sequencing mitochondrial, plastid, and nuclear loci from parasite/host pairs from throughout the parasite's range and with prior information from completely assembled mitochondrial and plastid genomes, we detected ten HGTs of five mitochondrial genes. Key Results: The ten HGTs appear to have occurred sequentially as C. coccineum expanded from East to West. Molecular-clock models yield Cynomorium stem ages between 66 and 156 Myr, with relaxed clocks converging on 66–67 Myr. Chinese Sapindales, probably Nitraria, were the first source of transferred genes, followed by Iranian and Mediterranean Caryophyllales. The most recently acquired gene appears to come from a Tamarix host in the Iberian Peninsula. Conclusion: Data on HGTs that have accumulated over the past 15 years, along with this discovery of multiple HGTs within a single widespread species, underline the need for more whole-genome data from parasite/host pairs to investigate if and how transferred copies coexist with, or replace, native functional genes. In compliance with data protection regulations, you may request that we remove your personal registration details at any time. (Use the following URL: https://www.editorialmanager.com/ajb/login.asp?a=r) Please contact the publication office if you have any questions.
Horizontal gene transfer is the main driver of antimicrobial resistance in broiler chicks infected with Salmonella enterica serovar Heidelberg
<p>Overuse and misuse of antibiotics in clinical settings and in food production have been linked to the increased prevalence and spread of antimicrobial resistance (AR). Consequently, public health and consumer concerns have resulted in a remarkable reduction in antibiotics used for food animal production. However, there are no data on the effectiveness of antibiotic removal in reducing AR shared through horizontal gene transfer (HGT). In this study, we used neonatal broiler chicks and Salmonella enterica serovar Heidelberg (SH), a model food pathogen, to test if chicks raised antibiotic-free harbor transferable AR. We challenged chicks with an antibiotic susceptible SH strain using various routes of inoculation and determined if SH isolates recovered carried plasmids conferring AR. We used antimicrobial susceptibility testing and whole genome sequencing (WGS) to show that chicks grown without antibiotics harbored antimicrobial resistant SH population 14 days after challenge and chicks challenged orally acquired AR at a higher rate than chicks inoculated via the cloaca. Using 16S rRNA gene sequencing we found that SH infection perturbed the microbiota of broiler chicks and used metagenomics and WGS to confirm commensal Escherichia coli population as the main reservoir of IncI1 plasmid acquired by SH. The carriage of this IncI1 plasmid posed no fitness cost to SH but increased its fitness when exposed to acidic pH in vitro. These results suggest that HGT of plasmids carrying AR shaped the evolution of SH and that antibiotic use reduction alone is insufficient to limit antibiotic resistance transfer from commensal bacteria to Salmonella.</p>
Hoarding and horizontal transfer led to an expanded gene and intron repertoire in the plastid genome of the diatom, Toxarium undulatum (Bacillariophyta)
<p>Multiple sequence alignments used to produce Figure 2</p>
Evolutionary "crowdsourcing": alignment of fitness landscapes allows for cross-species adaptation of a horizontally transferred gene
<p>This repository accompanies the publication of <i><strong>Evolutionary "crowdsourcing": alignment of fitness landscapes allows for cross-species adaptation of a horizontally transferred gene</strong></i> by Kosterlitz et. al. This research project explores the cross-species adaptation of a horizontally transferred gene through evolutionary "crowdsourcing." The repository provides all relevant data, code, and figures associated with the publication, enabling users to replicate the results and explore the findings in-depth.</p>
BactPrep: A user-friendly whole-genome sequencing analysis platform for the detection of homologous recombination and horizontal gene transfer in bacteria - Sample Dataset
<p>This is the dataset used as the sample dataset for the pipeline BactPrep. This dataset consists of 218 <em>Streptococcus pneumoniae</em> PMEN1 WGS assemblies collected from the year 1984 - 2008 from 22 unique countries globally. The raw sequencing data was originally published in the work: Rapid pneumococcal evolution in response to clinical interventions (doi: 10.1371/journal.ppat.1002745) under the bioproject PRJEB2085.</p> <p>We have assembled the raw sequences records with the following steps: 1) raw reads were first quality checked using fastQC 0.11.9; 2) adapters and low quality reads were removed using Trimmomatic 0.39 with parameter “ILLUMINACLIP:TruSeq2-PE.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36”; 3) trimmed reads were error-corrected and assembled into WGS assemblies using SPAdes 3.15.0 with parameters "--careful --mismatch-correction”.</p>
Data from: Systematic evaluation of horizontal gene transfer between eukaryotes and viruses
<p class="Authors">Gene exchange between viruses and their hosts acts as a key facilitator of horizontal gene transfer and is hypothesized to be a major driver of evolutionary change. Our understanding of this process comes primarily from bacteria and phage co-evolution, but the mode and functional importance of gene transfers between eukaryotes and their viruses remains anecdotal. Here we systematically characterized viral-eukaryotic gene exchange across eukaryotic and viral diversity, identifying thousands of transfers, and revealing their frequency, taxonomic distribution, and projected functions. Eukaryote-derived viral genes, abundant in the Nucleocytoviricota, highlighted common strategies for viral host-manipulation, including metabolic reprogramming, proteolytic degradation, and extracellular modification. Furthermore, viral-derived eukaryotic genes implicate genetic exchange in the early evolution and diversification of eukaryotes, particularly through viral-derived glycosyltransferases, which have impacted structures as diverse as algal cell walls, trypanosome mitochondria, and animal tissues. These findings illuminate the nature of viral-eukaryotic gene exchange and its impact on the evolution of viruses and their eukaryotic hosts.</p>
Data from: Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection
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Horizontal gene transfer is the main driver of antimicrobial resistance in broiler chicks infected with Salmonella enterica serovar Heidelberg
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Data from: Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis
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