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18 results for “lateral gene transfer”
Lateral gene transfer generates accessory genes that accumulate at different rates within a grass lineage
<p><span></span></p> <p>Lateral gene transfer (LGT) is the <span>movement</span> of DNA between <span>organism</span> without sexual <span>reproduction. </span>The acquired genes represent genetic novelties that <span>have</span> independently evolved in the donor<span>'</span>s genome. <span>Phylogenetic</span> methods <span>have</span> shown that LGT is widespread across the entire grass family, although we know little about the underlying dynamics.</p> <p>We identify laterally acquired genes in five de novo reference genomes from the same grass genus (four <em>Alloteropsis semialata</em> and one <em>Alloteropsis angusta</em>). Using additional resequencing data for a further 40 Alloteropsis individuals, we place the acquisition of each gene onto a phylogeny using stochastic character mapping, and then infer rates of gains and losses.</p> <p>We detect 168 laterally acquired genes in the five reference genomes [32-100 per genome]. Exponential decay models indicate that the rate of LGT acquisitions [6-28 per Ma] and subsequent losses [11-24% per Ma] varied significantly among lineages. Laterally acquired genes were lost at a higher rate than vertically inherited loci [0.02-0.8% per Ma].</p> <p>This high turnover creates intraspecific gene content variation, with a preponderance of them occurring as accessory genes in the <em>Alloteropsis</em> pangenome. This rapid turnover generates standing variation that can ultimately fuel local adaptation.</p>
Lateral gene transfer generates accessory genes that accumulate at different rates within a grass lineage
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Data from: Grafting or pruning in the animal tree: lateral gene transfer and gene loss?
Background: Lateral gene transfer (LGT), also known as horizontal gene transfer, into multicellular eukaryotes with differentiated tissues, particularly gonads, continues to be met with skepticism by many prominent evolutionary and genomic biologists. A detailed examination of 26 animal genomes identified putative LGTs in invertebrate and vertebrate genomes, concluding that there are fewer predicted LGTs in vertebrates/chordates than invertebrates, but there is still evidence of LGT into chordates, including humans. More recently, a reanalysis of a subset of these putative LGTs into vertebrates concluded that there is not horizontal gene transfer in the human genome. One of the genes in dispute is an N-acyl-aromatic-L-amino acid amidohydrolase (ENSG00000132744), which encodes ACY3. This gene was initially identified as a putative bacteria-chordate LGT but was later debunked as it has a significant BLAST match to a more recently deposited genome of Saccoglossus kowalevskii, a flatworm, Metazoan, and hemichordate. Results: Using BLAST searches, HMM searches, and phylogenetics to assess the evidence for LGT, gene loss, and rate variation in ACY3/ASPA homologues, the most parsimonious explanation for the distribution of ACY3/ASPA genes in eukaryotes involves both gene loss and bacteria-animal LGT, albeit LGT that occurred hundreds of millions of years ago prior to the divergence of gnathostomes. Conclusions: ACY3/ASPA is most likely a bacteria-animal LGT. LGTs at these time scales in the ancestors of humans are not unexpected given the many known, well-characterized, and adaptive LGTs from bacteria to insects and nematodes.
Data from: A laterally transferred viral gene modifies aphid wing plasticity
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Data from: Grafting or pruning in the animal tree: lateral gene transfer and gene loss?
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Data from: Recent events dominate interdomain lateral gene transfers between prokaryotes and eukaryotes and, with the exception of endosymbiotic gene transfers, few ancient transfer events persist
While there is compelling evidence for the impact of endosymbiotic gene transfer (EGT; transfer from either mitochondrion or chloroplast to the nucleus) on genome evolution in eukaryotes, the role of interdomain transfer from bacteria and/or archaea (i.e. prokaryotes) is less clear. Lateral gene transfers (LGTs) have been argued to be potential sources of phylogenetic information, particularly for reconstructing deep nodes that are difficult to recover with traditional phylogenetic methods. We sought to identify interdomain LGTs by using a phylogenomic pipeline that generated 13 465 single gene trees and included up to 487 eukaryotes, 303 bacteria and 118 archaea. Our goals include searching for LGTs that unite major eukaryotic clades, and describing the relative contributions of LGT and EGT across the eukaryotic tree of life. Given the difficulties in interpreting single gene trees that aim to capture the approximately 1.8 billion years of eukaryotic evolution, we focus on presence–absence data to identify interdomain transfer events. Specifically, we identify 1138 genes found only in prokaryotes and representatives of three or fewer major clades of eukaryotes (e.g. Amoebozoa, Archaeplastida, Excavata, Opisthokonta, SAR and orphan lineages). The majority of these genes have phylogenetic patterns that are consistent with recent interdomain LGTs and, with the notable exception of EGTs involving photosynthetic eukaryotes, we detect few ancient interdomain LGTs. These analyses suggest that LGTs have probably occurred throughout the history of eukaryotes, but that ancient events are not maintained unless they are associated with endosymbiotic gene transfer among photosynthetic lineages.
Data from: Lateral gene transfer from the dead
In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along the phylogeny traced by the ancestors of extant species. In the presence of lateral gene transfer (LGT), however, this may not be the case, because the species lineage from which a gene was transferred may have gone extinct or not have been sampled. Because it is not feasible to specify or reconstruct the complete phylogeny of all species, we must describe the evolution of genes outside the represented phylogeny by modelling the speciation dynamics that gave rise to the complete phylogeny. We demonstrate that if the number of sampled species is small compared to the total number of existing species, the overwhelming majority of gene transfers involve speciation to, and evolution along extinct or unsampled lineages. We show that the evolution of genes along extinct or unsampled lineages can to good approximation be treated as those of independently evolving lineages described by a few global parameters. Using this result, we derive an algorithm to calculate the probability of a gene tree and recover the maximum likelihood reconciliation given the phylogeny of the sampled species. Examining 473 near universal gene families from 36 cyanobacteria, we find that nearly a third of transfer events − 28% – appear to have topological signatures of evolution along extinct species, but only approximately 6% of transfers trace their ancestry to before the common ancestor of the sampled cyanobacteria.
Data from: A Bayesian method for analyzing lateral gene transfer
Lateral gene transfer (LGT)—which transfers DNA between two non-vertically related individuals belonging to the same or different species—is recognized as a major force in prokaryotic evolution, and evidence of its impact on eukaryotic evolution is ever increasing. LGT has attracted much public attention for its potential to transfer pathogenic elements and antibiotic resistance in bacteria, and to transfer pesticide resistance from genetically modified crops to other plants. In a wider perspective, there is a growing body of studies highlighting the role of LGT in enabling organisms to occupy new niches or adapt to environmental changes. The challenge LGT poses to the standard tree-based conception of evolution is also being debated. Studies of LGT have, however, been severely limited by a lack of computational tools. The best currently available LGT algorithms are parsimony-based phylogenetic methods, which require a pre-computed gene tree and cannot choose between sometimes wildly differing most-parsimonious solutions. Moreover, in many studies, simple heuristics are applied that can only handle putative orthologs and completely disregard gene duplications. Consequently, proposed LGT among specific gene families, and the rate of LGT in general remain debated. We present a Bayesian MCMC-based method that integrates gene duplication, gene loss, LGT, and sequence evolution, and apply the method in a genome-wide analysis of two groups of bacteria: Mollicutes and Cyanobacteria. Our analyses show that although the LGT rate between distant species is high, the net combined rate of duplication and close species-LGT is on average higher. We also show that the common practice of disregarding reconcilability in gene tree inference overestimates the number of LGT and duplication events.
Data from: Low rates of lateral gene transfer among metabolic genes define the evolving biogeochemical niches of archaea through deep time
Phylogenomic analyses of archaeal genome sequences are providing windows into the group's evolutionary past, even though most archaeal taxa lack a conventional fossil record. Here, phylogenetic analyses were performed using key metabolic genes that define the metabolic niche of microorganisms. Such genes are generally considered to have undergone high rates of lateral gene transfer. Many gene sequences formed clades that were identical, or similar, to the tree constructed using large numbers of genes from the stable core of the genome. Surprisingly, such lateral transfer events were readily identified and quantifiable, occurring only a relatively small number of times in the archaeal domain of life. By placing gene acquisition events into a temporal framework, the rates by which new metabolic genes were acquired can be quantified. The highest lateral transfer rates were among cytochrome oxidase genes that use oxygen as a terminal electron acceptor (with a total of 12-14 lateral transfer events, or 3.4-4.0 events per billion years, across the entire archaeal domain). Genes involved in sulfur or nitrogen metabolism had much lower rates, on the order of one lateral transfer event per billion years. This suggests that lateral transfer rates of key metabolic proteins are rare and not rampant.
Data from: Assessing the effects of a sequestered germline on interdomain lateral gene transfer in Metazoa
A sequestered germline in Metazoa has been argued to be an obstacle to lateral gene transfer (LGT), though few studies have specifically assessed this claim. Here we test the hypothesis that the origin of a sequestered germline reduced LGT events in Bilateria (i.e. triploblast lineages) as compared to early-diverging Metazoa (i.e. Ctenophora, Cnidaria, Porifera, and Placozoa). We analyze single-gene phylogenies generated with over 900 species, sampled from among Bacteria, Archaea and Eukaryota to identify well-supported interdomain LGTs. We focus on interdomain LGT (i.e. those between prokaryotes and Metazoa) as systematic errors in single gene tree reconstruction create uncertainties for interpreting eukaryote-to-eukaryotes transfers. The breadth of the sampled Metazoa enables us to estimate the timing of LGTs, and to examine the pattern before vs. after the evolution of a sequestered germline. We identified 58 LGTs found only in Metazoa and prokaryotes (i.e. bacteria and/or archaea), and 7 genes transferred from prokaryotes into Metazoa plus one other eukaryotic clade. Our analyses indicate that more interdomain transfers occurred before the development of a sequestered germline, consistent with the hypothesis that this feature is an obstacle to LGT.
Data from: A recently transferred cluster of bacterial genes in Trichomonas vaginalis –lateral gene transfer and the fate of acquired genes.
Background: Lateral Gene Transfer (LGT) has recently gained recognition as an important contributor to some eukaryote proteomes, but the mechanisms of acquisition and fixation in eukaryotic genomes are still uncertain. A previously defined norm for LGTs in microbial eukaryotes states that the majority are genes involved in metabolism, the LGTs are typically localized one by one, surrounded by vertically inherited genes on the chromosome, and phylogenetics shows that a broad collection of bacterial lineages have contributed to the transferome. Results: A unique 34 kbp long fragment with 27 clustered genes (TvLF) of prokaryote origin was identified in the sequenced genome of the protozoan parasite Trichomonas vaginalis. Using a PCR based approach we confirmed the presence of the orthologous fragment in four additional T. vaginalis strains. Detailed sequence analyses unambiguously suggest that TvLF is the result of one single, recent LGT event. The proposed donor is a close relative to the firmicute bacterium Peptoniphilus harei. High nucleotide sequence similarity between T. vaginalis strains, as well as to P. harei, and the absence of homologs in other Trichomonas species, suggests that the transfer event took place after the radiation of the genus Trichomonas. Some genes have undergone pseudogenization and degradation, indicating that they may not be retained in the future. Functional annotations reveal that genes involved in informational processes are particularly prone to degradation. Conclusions: We conclude that, although the majority of eukaryote LGTs are single gene occurrences, they may be acquired in clusters of several genes that are subsequently cleansed of evolutionarily less advantageous genes.
Data from: Lateral gene transfer from the dead
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Data from: Recent events dominate interdomain lateral gene transfers between prokaryotes and eukaryotes and, with the exception of endosymbiotic gene transfers, few ancient transfer events persist
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Data from: A recently transferred cluster of bacterial genes in Trichomonas vaginalis –lateral gene transfer and the fate of acquired genes.
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Data from: Assessing the effects of a sequestered germline on interdomain lateral gene transfer in Metazoa
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Data from: A Bayesian method for analyzing lateral gene transfer
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Data from: Low rates of lateral gene transfer among metabolic genes define the evolving biogeochemical niches of archaea through deep time
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Data from: Adaptive evolution of C4 photosynthesis through recurrent lateral gene transfer
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