scholarly journals Horizontal gene transfer in 44 early diverging fungi favors short, metabolic, extracellular proteins from associated bacteria

2021 ◽  
Author(s):  
Michał Ciach ◽  
Julia Pawłowska ◽  
Anna Muszewska
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Phylogenetic Trees ◽  
Large Scale ◽  
Genetic Material ◽  
Small Sample ◽  
Extracellular Proteins ◽  
Gene Exchange ◽  
Statistical Sample

AbstractNumerous studies have been devoted to individual cases of horizontally acquired genes in fungi. It has been shown that such genes expand their metabolic capabilities and contribute to their adaptations as parasites or symbionts. Some studies have provided a more extensive characterization of the horizontal gene transfer (HGT) in Dikarya. However, in the early diverging fungi (EDF), the overall influence of HGT on the ecological adaptation and evolution is largely unknown. In order to fill this gap, we have designed a computational pipeline to obtain a sample of over 600 phylogenetic trees with evidence for recent to moderately old HGT across multiple EDF genomes ranging from Chytridiomycota and Blastocladiomycota to Mucoromycota. Our pipeline is designed to obtain a small sample of reliable HGT events with a possibly minimal number of false detections that distort the overall statistical patterns. We show that transfer rates differ greatly between closely related species and strains, but the ancestrally aquatic fungi are generally more likely to acquire foreign genetic material than terrestrial ones. A close ecological relationship with another organism is a predisposing condition, but does not always result in an extensive gene exchange, with some fungal lineages showing a preference for HGT from loosely associated soil bacteria.ImportanceAlthough it is now recognized that horizontal gene exchange is a factor influencing the adaptation and evolution of eukaryotic organisms, the so far described cases in early diverging fungi (EDF) are fragmentary, and a large-scale comprehensive study is lacking. We have designed a methodology to obtain a reliable, statistical sample of inter-kingdom xenologs across the tree of life of EDF to give a preliminary characterization of their general properties and patterns. We study how different fungal lineages vary in terms of the number of xenologs, what are their ecological associations, and the molecular properties of proteins encoded by the acquired genes. Our results help to better understand to what extent and in what way the incorporation of foreign genetic material shaped the present biodiversity of fungi.

scholarly journals What do we gain when tolerating loss? The information bottleneck, lossy compression, and detecting horizontal gene transfer

2021 ◽  
Author(s):  
Apurva Narechania ◽  
Rob DeSalle ◽  
Barun Mathema ◽  
Barry N Kreiswirth ◽  
Paul J Planet
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Language Processing ◽  
Large Scale ◽  
Genetic Material ◽  
Joint Probability ◽  
Rate Distortion ◽  
Joint Probability Distribution ◽  
Model Free ◽  
Information Bottleneck

Most microbes have the capacity to acquire genetic material from their environment. Recombination of foreign DNA yields genomes that are, at least in part, incongruent with the vertical history of their species. Dominant approaches for detecting such horizontal gene transfer (HGT) and recombination are phylogenetic, requiring a painstaking series of analyses including sequence-based clustering, alignment, and phylogenetic tree reconstruction. Given the breakneck pace of genome sequencing, these traditional pan-genomic methods do not scale. Here we propose an alignment-free and tree-free technique based on the sequential information bottleneck (SIB), an optimization procedure designed to extract some portion of relevant information from one random variable conditioned on another. In our case, this joint probability distribution tabulates occurrence counts of k-mers with respect to their genomes of origin (the relevance information) with the expectation that HGT and recombination will create a strong signal that distinguishes certain sets of co-occuring k-mers. The technique is conceptualized as a rate-distortion problem. We measure distortion in the relevance information as k-mers are compressed into clusters based on their co-occurrence in the source genomes. This approach is similar to topic mining in the Natural Language Processing (NLP) literature. The result is model-free, unsupervised compression of k-mers into genomic topics that trace tracts of shared genome sequence whether vertically or horizontally acquired. We examine the performance of SIB on simulated data and on the known large-scale recombination event that formed the Staphylococcus aureus ST239 clade. We use this technique to detect recombined regions and recover the vertically inherited core genome with a fraction of the computing power required of current phylogenetic methods.

scholarly journals Plasmid Characteristics Modulate the Propensity of Gene Exchange in Bacterial Vesicles

2019 ◽  
Vol 201 (7) ◽  
Author(s):  
Frances Tran ◽  
James Q. Boedicker
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Extracellular Vesicles ◽  
Copy Number ◽  
Genetic Material ◽  
Plasmid Copy Number ◽  
Gene Exchange ◽  
Origin Of Replication ◽  
Plasmid Copy ◽  
The Impact

ABSTRACTHorizontal gene transfer is responsible for the exchange of many types of genetic elements, including plasmids. Properties of the exchanged genetic element are known to influence the efficiency of transfer via the mechanisms of conjugation, transduction, and transformation. Recently, an alternative general pathway of horizontal gene transfer has been identified, namely, gene exchange by extracellular vesicles. Although extracellular vesicles have been shown to facilitate the exchange of several types of plasmids, the influence of plasmid characteristics on genetic exchange within vesicles is unclear. Here, a set of different plasmids was constructed to systematically test the impact of plasmid properties, specifically, plasmid copy number, size, and origin of replication, on gene transfer in vesicles. The influence of each property on the production, packaging, and uptake of vesicles containing bacterial plasmids was quantified, revealing how plasmid properties modulate vesicle-mediated horizontal gene transfer. The loading of plasmids into vesicles correlates with the plasmid copy number and is influenced by characteristics that help set the number of plasmids within a cell, including size and origin of replication. Plasmid origin also has a separate impact on both vesicle loading and uptake, demonstrating that the origin of replication is a major determinant of the propensity of specific plasmids to transfer within extracellular vesicles.IMPORTANCEExtracellular vesicle formation and exchange are common within bacterial populations. Vesicles package multiple types of biomolecules, including genetic material. The exchange of extracellular vesicles containing genetic material facilitates interspecies DNA transfer and may be a promiscuous mechanism of horizontal gene transfer. Unlike other mechanisms of horizontal gene transfer, it is unclear whether characteristics of the exchanged DNA impact the likelihood of transfer in vesicles. Here, we systematically examine the influence of plasmid copy number, size, and origin of replication on the loading of DNA into vesicles and the uptake of DNA containing vesicles by recipient cells. These results reveal how each plasmid characteristic impacts gene transfer in vesicles and contribute to a greater understanding of the importance of vesicle-mediated gene exchange in the landscape of horizontal gene transfer.

scholarly journals Evidence of horizontal gene transfer between land plant plastids has surprising conservation implications

2021 ◽  
Author(s):  
Lars Hedenäs ◽  
Petter Larsson ◽  
Bodil Cronholm ◽  
Irene Bisang
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Large Scale ◽  
Incomplete Lineage Sorting ◽  
Genetic Material ◽  
Land Plant ◽  
Internal Transcribed Spacers ◽  
Time Interval ◽  
Moss Species ◽  
Plastid Genomes

Abstract Background and Aims Horizontal Gene Transfer (HGT) is an important evolutionary mechanism because it transfers genetic material that may code for traits or functions, between species or genomes. It is frequent in mitochondrial and nuclear genomes but has not been demonstrated between plastid genomes of different green land plant species. Methods We Sanger sequenced the nuclear Internal transcribed spacers 1&2 (ITS) and the plastid rpl16 G2 intron (rpl16). In five individuals with foreign rpl16 we also sequenced atpB-rbcL and trnLUAA-trnFGAA. Key Results We discovered 14 individuals of a moss species with typical nuclear ITS but foreign plastid rpl16, from a species of a distant lineage. None of the individuals with three plastid markers sequenced contained all foreign markers, demonstrating the transfer of plastid fragments rather than of the entire plastid genome, i.e., entire plastids were not transferred. The two lineages diverged 165185 Myr BP. The extended time interval since lineage divergence suggests that the foreign rpl16 is more likely explained by HGT than by hybridisation or incomplete lineage sorting. Conclusions We provide the first conclusive evidence of interspecific plastid-to-plastid HGT among land plants. Two aspects are critical: it occurred at several localities during the massive colonization of recently disturbed open habitats that were created by large-scale liming as a freshwater biodiversity conservation measure. It also involved mosses whose unique life cycle includes spores that first develop a filamentous protonema phase. We hypothesize that gene transfer is facilitated when protonema filaments of different species intermix intimately when colonizing disturbed early succession habitats.

scholarly journals Detecting Horizontal Gene Transfer by Mapping Sequencing Reads Across Species Boundaries

2016 ◽  
Author(s):  
Kathrin Trappe ◽  
Tobias Marschall ◽  
Bernhard Y. Renard
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Phylogenetic Trees ◽  
Genetic Material ◽  
Real Data ◽  
A Genome ◽  
Split Read ◽  
Candidate Regions ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data

AbstractHorizontal gene transfer (HGT) is a fundamental mechanism that enables organisms such as bacteria to directly transfer genetic material between distant species. This way, bacteria can acquire new traits such as antibiotic resistance or pathogenic toxins. Current bioinfor-matics approaches focus on the detection of past HGT events by exploring phylogenetic trees or genome composition inconsistencies. However, this normally requires the availability of finished and fully annotated genomes and of sufficiently large deviations that allow detection. Thus, these techniques are not widely applicable. Especially in an outbreak scenario where new HGT mediated pathogens emerge, there is need for fast and precise HGT detection. Next-generation sequencing (NGS) technologies can facilitate swift analysis of unknown pathogens but, to the best of our knowledge, so far no approach uses NGS data directly to detect HGTs.We present Daisy, a novel mapping-based tool for HGT detection directly from NGS data. Daisy determines HGT boundaries with split-read mapping and evaluates candidate regions relying on read pair and coverage information. Daisy can successfully detect HGT regions with base pair resolution in both simulated and real data, and outperforms alternative approaches using a genome assembly of the reads. We see our approach as a powerful complement for a comprehensive analysis of HGT in the context of NGS data. Daisy is freely available fromhttp://github.com/ktrappe/daisy.

scholarly journals Horizontal Gene Transfer Involving Chloroplasts

2021 ◽  
Vol 22 (9) ◽  
pp. 4484
Author(s):  
Ewa Filip ◽  
Lidia Skuza
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Driving Force ◽  
Genetic Material ◽  
Adaptive Significance ◽  
Chloroplast Genomes ◽  
Organelle Genomes ◽  
Number Of Genes ◽  
Cellular Compartments

Horizontal gene transfer (HGT)- is defined as the acquisition of genetic material from another organism. However, recent findings indicate a possible role of HGT in the acquisition of traits with adaptive significance, suggesting that HGT is an important driving force in the evolution of eukaryotes as well as prokaryotes. It has been noted that, in eukaryotes, HGT is more prevalent than originally thought. Mitochondria and chloroplasts lost a large number of genes after their respective endosymbiotic events occurred. Even after this major content loss, organelle genomes still continue to lose their own genes. Many of these are subsequently acquired by intracellular gene transfer from the original plastid. The aim of our review was to elucidate the role of chloroplasts in the transfer of genes. This review also explores gene transfer involving mitochondrial and nuclear genomes, though recent studies indicate that chloroplast genomes are far more active in HGT as compared to these other two DNA-containing cellular compartments.

scholarly journals Molecular and biochemical characterization of an endo-β-1,3-glucanase from the pinewood nematode Bursaphelenchus xylophilus acquired by horizontal gene transfer from bacteria

2005 ◽  
Vol 389 (1) ◽  
pp. 117-125 ◽  
Author(s):  
Taisei KIKUCHI ◽  
Hajime SHIBUYA ◽  
John T. JONES
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Biochemical Characterization ◽  
Glycosyl Hydrolase ◽  
Functional Characterization ◽  
Nematode Species ◽  
Bursaphelenchus Xylophilus ◽  
Pinewood Nematode ◽  
Sequence Comparisons

We report the cloning and functional characterization of an endo-β-1,3-glucanase from the pinewood nematode Bursaphelenchus xylophilus acquired by horizontal gene transfer from bacteria. This is the first gene of this type from any nematode species. We show that a similar cDNA is also present in another closely related species B. mucronatus, but that similar sequences are not present in any other nematode studied to date. The B. xylophilus gene is expressed solely in the oesophageal gland cells of the nematode and the protein is present in the nematode's secretions. The deduced amino acid sequence of the gene is very similar to glycosyl hydrolase family 16 proteins. The recombinant protein, expressed in Escherichia coli, preferentially hydrolysed the β-1,3-glucan laminarin, and had very low levels of activity on β-1,3-1,4-glucan, lichenan and barley β-glucan. Laminarin was degraded in an endoglucanase mode by the enzyme. The optimal temperature and pH for activity of the recombinant enzyme were 65 °C and pH 4.9. The protein is probably important in allowing the nematodes to feed on fungi. Sequence comparisons suggest that the gene encoding the endo-β-1,3-glucanase was acquired by horizontal gene transfer from bacteria. B. xylophilus therefore contains genes that have been acquired by this process from both bacteria and fungi. These findings support the idea that multiple independent horizontal gene transfer events have helped in shaping the evolution of several different life strategies in nematodes.

scholarly journals Involvement of plastid, mitochondrial and nuclear genomes in plant-to-plant horizontal gene transfer

2014 ◽  
Vol 83 (4) ◽  
pp. 317-323 ◽  
Author(s):  
Maria Virginia Sanchez-Puerta
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Plant Mitochondria ◽  
Genetic Material ◽  
Single Copy ◽  
Convincing Evidence ◽  
Cell Contact ◽  
Plant Mtdna ◽  
Nuclear Genomes ◽  
Foreign Genes

This review focuses on plant-to-plant horizontal gene transfer (HGT) involving the three DNA-containing cellular compartments. It highlights the great incidence of HGT in the mitochondrial genome (mtDNA) of angiosperms, the increasing number of examples in plant nuclear genomes, and the lack of any convincing evidence for HGT in the well-studied plastid genome of land plants. Most of the foreign mitochondrial genes are non-functional, generally found as pseudogenes in the recipient plant mtDNA that maintains its functional native genes. The few exceptions involve chimeric HGT, in which foreign and native copies recombine leading to a functional and single copy of the gene. Maintenance of foreign genes in plant mitochondria is probably the result of genetic drift, but a possible evolutionary advantage may be conferred through the generation of genetic diversity by gene conversion between native and foreign copies. Conversely, a few cases of nuclear HGT in plants involve functional transfers of novel genes that resulted in adaptive evolution. Direct cell-to-cell contact between plants (e.g. host-parasite relationships or natural grafting) facilitate the exchange of genetic material, in which HGT has been reported for both nuclear and mitochondrial genomes, and in the form of genomic DNA, instead of RNA. A thorough review of the literature indicates that HGT in mitochondrial and nuclear genomes of angiosperms is much more frequent than previously expected and that the evolutionary impact and mechanisms underlying plant-to-plant HGT remain to be uncovered.

scholarly journals Trasposon Mediated Horizontal Gene Transfer (T-HGT) of Circulating Tumor DNA Reshapes MM Clonal Architecture

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 3065-3065
Author(s):  
Munevver Cinar ◽  
Steven Flygare ◽  
Marina Mosunjac ◽  
Ganji Nagaraju ◽  
Dongkyoo Park ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Drug Sensitivity ◽  
Genetic Material ◽  
Host Cells ◽  
Response To Treatment ◽  
Hierarchical Architecture ◽  
Tumor Evolution ◽  
Sequencing Analysis

Spatial genetic heterogeneity is a characteristic phenomenon that influences multiple myeloma's (MM) phenotype and drug sensitivity (Rasche L. et al and Bolli N et al.). Hence, the branch model of tumor evolution is not sufficient to explain the disorganized architecture observed in MM. In this study, we investigated whether MM ctDNA horizontal gene transfer (HGT) affect tumor genetic architecture and drug sensitivity, resembling what is seen in prokaryotes, and elucidated the mechanisms involved in the mobilization of genetic material from one cell to another. We identified that plasma from patients with MM transmits drug sensitivity or resistance to cells in culture. This transmission of drug sensitivity is mediated by ctDNA transfer of oncogenes to a host cell. Importantly, in vitro and in vivo demonstrated that ctDNA mainly targets cells resembling the cell of origin (tropism). Karyotype spreads and whole genome sequencing demonstrated that once patients ctDNA encounters host cells, it migrates into the nucleus where it ultimately integrates into the cell's genome. Integration to the genome was confirmed to be targeted to myeloma cells. Further sequencing analysis of multiple MM samples identified ctDNA tropism and integration is dependent on the 5' and 3' end presence of transposable elements (TE), particularly of the MIR and ALUsq family. These results were further validated by TE mediated delivery of GFP into MM cells in vitro and HSVTK in tumors of mouse xenografts. In conclusion, this data indicates for the first time that TE mediates MM ctDNA HGT into homologous tumor cells shaping the hierarchical architecture of tumor clones and affecting tumor response to treatment. Therapeutically, this unique quality of ctDNA can be exploited for targeted gene therapeutic approaches in MM and potentially other cancers. Disclosures Bernal-Mizrachi: Kodikas Therapeutic Solutions, Inc: Equity Ownership; TAKEDA: Research Funding; Winship Cancer Institute: Employment, Patents & Royalties.

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