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78 results for “Horizontal transfer”
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>
Part 3: Dataset and script for a manuscript entitled 'Host-specific subtelomere: structural variation and horizontal transfer in asexual filamentous fungal pathogens'
<p>Datasets, scripts and instructions for reproducing some of the results in the manuscript. The file subtelomere.tar needs to be unpacked on a Linux system. After unpacking it, go to the directory subtelomere, which contains a number of subdirectories. One subdirectory is named data, which contains genome assemblies and is used to hold datasets of short reads; the datasets of short reads in the files Data.One.Focb.tar, Data.One.Focb-2.tar and reads.tar on the four-part depository need to be placed in the subdirectory subtelomere/data/reads/.</p> <p>The other subdirectories in the directory subtelomere contain instructions and scripts for reproducing many of the results in the manuscript. The subdirectory subtelomere/TwoCopies/ contains two subdirectories of instructions and scripts for reproducing the results in the table on the average coverage of Focb TR4 isolates. The subdirectory subtelomere/TEs/ contains four subdirectories, each of which provides instructions and scripts for estimating the copy numbers of one or two transposons in the table on the copy numbers of five transposons in Focb TR4 isolates. The subdirectory subtelomere/SVs/ explains how the results on SNPs and presence/absence polymorphisms could be reproduced. The subdirectory subtelomere/Fol/ contains three subdirectories, each of which includes information for reproducing one of the three columns in the table on mean SNP rates between Fol D11 and each of Fol4287, Fol069 and Fol072. The subdirectory subtelomere/Forc/ demonstrates how some of the programs and scripts developed by the author are used to analyze a genome assembly of Forc isolate Forc016. The subdirectory subtelomere/pub/ contains the source and executable code of those programs. See the README and z.cmd files in each leaf subdirectory for more information</p>
Transposon DNA sequences facilitate the tissue-specific horizontal transfer: te expression supplementary datasets
<p>These datasets contain data on analyses of TE expression stability. Raw RNA seq counts were processed using DESeq2 R package. Low count genes and TEs were removed. Counts across samples were normalized for library sizes and log-transformed using 'regularized log' transformation. Batch normalization was performed on log-transformed data with ComBat function from sva R package. Expression variability (EV) of TEs and genes (probes) was estimated using the previously described method [1, 2].</p> <p>1. Bashkeel, N., Perkins, T.J., Kærn, M. et al. Human gene expression variability and its dependence on methylation and aging. BMC Genomics 20, 941 (2019). https://doi.org/10.1186/s12864-019-6308-7<br> 2. Alemu EY, Carl JW Jr, Corrada Bravo H, Hannenhalli S. Determinants of expression variability. Nucleic Acids Res. 2014;42(6):3503-3514. doi:10.1093/nar/gkt1364</p> <p> </p> <p>PC.zip - the results of TE expression and stability in prostate cancer.</p> <ul> <li>0.PC.RlogMAD.pdf - count barplots for TE identified with MAD criteria</li> <li>0.PC.RlogSD.pdf - count barplots for TE identified with SD criteria</li> <li>0.PC.TE.rlogcpm.mad.xls -stability measures according MAD (median absolute deviance) criteria </li> <li>0.PC.TE.rlogcpm.sd.xls - stability measures according SD criteria </li> <li>0.PC_TE_bootstrap.pdf - TE expression stability</li> <li>PC.deseq.logCPM.csv - TE log transformed expression matrix </li> <li>PC.TE_count_table.csv - TE raw count matrix </li> <li>PC_Deseq2data.Rdata - R data object with deseq objet, raw and normalized counts</li> </ul> <p> </p> <p>MM.zip - the results of TE expression and stability in multiple myeloma.</p> <ul> <li>0.MM.RlogMAD.pdf - count barplots for TE identified with MAD criteria</li> <li>0.MM.RlogSD.pdf - count barplots for TE identified with SD criteria</li> <li>0.MM_TE_bootstrap.pdf - TE expression stability</li> <li>MM.deseq.logCPM.csv - TE raw count matrix </li> <li>MM.rlog.mad.xlsx- stability measures according MAD (median absolute deviance) criteria</li> <li>MM.rlog.sd.xlsx - stability measures according MAD (median absolute deviance) criteria </li> <li>MM.TE_count_table.csv - TE raw count matrix </li> <li>Myeloma_Deseq2data.Rdata - R data object with deseq objet, raw and normalized counts</li> </ul>
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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Genetic variability, community structure, and horizontal transfer of endosymbionts among three Asia II‐Bemisia tabaci mitotypes in Pakistan
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Data from: Sequential horizontal gene transfers from different hosts in a widespread Eurasian parasitic plant, Cynomorium coccineum
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Data from: Establishment and maintenance of aphid endosymbionts after horizontal transfer is dependent on host genotype
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Data from: Horizontal gene transfer constrains the timing of methanogen evolution
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Data from: Horizontal gene transfer of acetyltransferases, invertases and chorismate mutases from different bacteria to diverse recipients
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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
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Data from: Systematic evaluation of horizontal gene transfer between eukaryotes and viruses
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Evolution of an insect immune barrier through horizontal gene transfer mediated by a parasitic wasp
<p>Numerical data that underlies tables and graphs (figures 1-7, 9, 10; table 1) and statistics of the PLOS Genetics article from Di Lelio et al., 2019.</p>
Data from: The genomes of polyextremophilic Cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions
The role and extent of horizontal gene transfer (HGT) in eukaryotes are hotly disputed topics that impact our understanding of the origin of metabolic processes and the role of organelles in cellular evolution. We addressed this issue by analyzing 10 novel Cyanidiales genomes and determined that 1% of their gene inventory is HGT-derived. Numerous HGT candidates share a close phylogenetic relationship with prokaryotes that live in similar habitats as the Cyanidiales and encode functions related to polyextremophily. HGT candidates differ from native genes in GC-content, number of splice sites, and gene expression. HGT candidates are more prone to loss, which may explain the absence of a eukaryotic pan-genome. Therefore, the lack of a pan-genome and cumulative effects fail to provide substantive arguments against our hypothesis of recurring HGT followed by differential loss in eukaryotes. The maintenance of 1% HGTs, even under selection for genome reduction, underlines the importance of non-endosymbiosis related foreign gene acquisition.
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