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At least 1,315 records · Page 73Linked to original sources
PubMed2005

Mobile genetic elements: the agents of open source evolution.

Horizontal genomics is a new field in prokaryotic biology that is focused on the analysis of DNA sequences in prokaryotic chromosomes that seem to have originated from other prokaryotes or eukaryotes. However, it is equally important to understand the agents that effect DNA movement: plasmids, bacteriophages and transposons. Although these agents occur in all prokaryotes, comprehensive genomics of the prokaryotic mobile gene pool or 'mobilome' lags behind other genomics initiatives owing to challenges that are distinct from cellular chromosomal analysis. Recent work shows promise of improved mobile genetic element (MGE) genomics and consequent opportunities to take advantage - and avoid the dangers - of these 'natural genetic engineers'. This review describes MGEs, their properties that are important in horizontal gene transfer, and current opportunities to advance MGE genomics.

Conjugation, Genetic↗
PubMed2006

Unifying measures of gene function and evolution.

Recent genome analyses revealed intriguing correlations between variables characterizing the functioning of a gene, such as expression level (EL), connectivity of genetic and protein-protein interaction networks, and knockout effect, and variables describing gene evolution, such as sequence evolution rate (ER) and propensity for gene loss. Typically, variables within each of these classes are positively correlated, e.g. products of highly expressed genes also have a propensity to be involved in many protein-protein interactions, whereas variables between classes are negatively correlated, e.g. highly expressed genes, on average, evolve slower than weakly expressed genes. Here, we describe principal component (PC) analysis of seven genome-related variables and propose biological interpretations for the first three PCs. The first PC reflects a gene's 'importance', or the 'status' of a gene in the genomic community, with positive contributions from knockout lethality, EL, number of protein-protein interaction partners and the number of paralogues, and negative contributions from sequence ER and gene loss propensity. The next two PCs define a plane that seems to reflect the functional and evolutionary plasticity of a gene. Specifically, PC2 can be interpreted as a gene's 'adaptability' whereby genes with high adaptability readily duplicate, have many genetic interaction partners and tend to be non-essential. PC3 also might reflect the role of a gene in organismal adaptation albeit with a negative rather than a positive contribution of genetic interactions; we provisionally designate this PC 'reactivity'. The interpretation of PC2 and PC3 as measures of a gene's plasticity is compatible with the observation that genes with high values of these PCs tend to be expressed in a condition- or tissue-specific manner. Functional classes of genes substantially vary in status, adaptability and reactivity, with the highest status characteristic of the translation system and cytoskeletal proteins, highest adaptability seen in cellular processes and signalling genes, and top reactivity characteristic of metabolic enzymes.

Animals↗
PubMed2026

Advances in CRISPR Base Editing: From Molecular Evolution to Therapeutic Applications in Genomic Medicine.

CRISPR-Cas9 systems revolutionized gene editing, but inherent drawbacks, namely DNA double-strand breaks (DSBs) and the difficulty of achieving precise repairs (due to low HDR efficiency), led researchers to invent new, more accurate gene editing tools. Base editing represents a significant leap forward, enabling targeted single-nucleotide conversions directly on the DNA without DSBs or donor templates. The core technology involves fusing catalytically dead or nickase Cas proteins to DNA deaminase enzymes. Cytosine base editors (CBEs) convert C•G to T•A pairs, while adenine base editors (ABEs) change A•T to G•C. These editors exploit the deaminase function within the R-loop structure formed by Cas binding and co-opt endogenous DNA repair mechanisms for precision. While offering improved efficiency and editing precision, base editing faces persistent challenges, such as off-target effects, bystander edits, delivery and ethical concerns. Continuous engineering efforts have refined these tools, enhancing accuracy, expanding targetability and reducing unwanted edits. The base editing arsenal has also broadened to include C-to-G base editors (CGBEs), dual A&C editors and versions targeting organelles. Successful preclinical studies demonstrating the correction of mutations responsible for the disease have paved the way for clinical trials, which are now testing therapies for conditions like sickle cell disease, β-thalassaemia and hypercholesterolemia using various delivery systems. This review explores CRISPR base editing's origins, mechanisms of action, potential therapies and current restrictions, pointing to its broadening impact on medical genetics.

Humans↗
PubMed2005

The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode.

Complete genome DNA sequence and analysis is presented for Wolbachia, the obligate alpha-proteobacterial endosymbiont required for fertility and survival of the human filarial parasitic nematode Brugia malayi. Although, quantitatively, the genome is even more degraded than those of closely related Rickettsia species, Wolbachia has retained more intact metabolic pathways. The ability to provide riboflavin, flavin adenine dinucleotide, heme, and nucleotides is likely to be Wolbachia's principal contribution to the mutualistic relationship, whereas the host nematode likely supplies amino acids required for Wolbachia growth. Genome comparison of the Wolbachia endosymbiont of B. malayi (wBm) with the Wolbachia endosymbiont of Drosophila melanogaster (wMel) shows that they share similar metabolic trends, although their genomes show a high degree of genome shuffling. In contrast to wMel, wBm contains no prophage and has a reduced level of repeated DNA. Both Wolbachia have lost a considerable number of membrane biogenesis genes that apparently make them unable to synthesize lipid A, the usual component of proteobacterial membranes. However, differences in their peptidoglycan structures may reflect the mutualistic lifestyle of wBm in contrast to the parasitic lifestyle of wMel. The smaller genome size of wBm, relative to wMel, may reflect the loss of genes required for infecting host cells and avoiding host defense systems. Analysis of this first sequenced endosymbiont genome from a filarial nematode provides insight into endosymbiont evolution and additionally provides new potential targets for elimination of cutaneous and lymphatic human filarial disease.

Animals↗
PubMed1997

Molecular evolution of the second ancient human mariner transposon, Hsmar2, illustrates patterns of neutral evolution in the human genome lineage.

A consensus sequence for the second ancient mariner identified in the human genome, Hsmar2, was constructed by majority rule from full-length and partial sequences of 44 of the +/-1000 copies in the genome. This 1300 base pair (bp) consensus has 31 bp imperfect terminal repeats (ITRs) and encodes a 351 amino acid (aa) mariner transposase. The sequence of this transposase has allowed classification of Hsmar2 as a basal lineage of the irritans subfamily of mariners, sharing at most 38% aa identity with other members of the subfamily. The individual copies in the human genome are all highly mutated from the consensus, having suffered numerous small and some large insertions and deletions (indels), including many insertions of S and J subfamily Alu elements. The copies differ, on average, from the consensus by 11.6%, have suffered 11.8 indels per kilobase (kb), and only 3.7% of the 30 hypermutable CpG dinucleotide pairs in the consensus remain intact. This level of divergence indicates that the ancestrally active Hsmar2 element represented by the consensus was present in the human genome lineage about 80 million years (Myr) ago. Each copy has apparently evolved since then largely independently of the others, and with little constraint on its transposase coding capacity. This pattern of molecular evolution fits the current model for mariner transposon evolution. These copies provide multiple independent datasets for evaluating the pattern of neutral evolution in the human genome, for example, they confirm that most indels are very short and that deletions are twice as common as insertions.

Amino Acid Sequence↗
PubMed2026

Enhancing detection of polygenic adaptation: a comparative study of machine learning and statistical approaches using simulated evolve-and-resequence data.

BACKGROUND: Detecting signals of polygenic adaptation remains a significant challenge in population genomics, as traditional methods often struggle to identify the associated subtle, multi-locus allele-frequency shifts. Here, we introduced and tested several novel approaches combining machine learning techniques with traditional statistical tests to detect polygenic adaptation patterns in time-series of allele frequency changes from whole genome data. We implemented a Naive Bayesian Classifier (NBC) and One-Class Support Vector Machines (OCSVM), and compared their performance against the classical Fisher's Exact Test (FET). Furthermore, we combined machine learning and statistical models (OCSVM-FET and NBC-FET), resulting in 5 competing approaches. The framework is mainly designed and validated for evolve-and-resequence (EaR) experimental designs, where defined selection pressures and temporal sampling are feasible, but might be applicable for certain natural experiments as well. RESULTS: Using a simulated dataset based on empirical C. riparius Pool-Seq data, we evaluated methods across evolutionary scenarios varying in generation, selection strength, and number of loci under selection. Our results demonstrate that the combined OCSVM-FET approach consistently outperformed competing methods, achieving the lowest false positive rate, highest area under the curve, and high accuracy. The performance peak aligned with what we term the 'late dynamic phase' of adaptation - the period after initial selection has occurred but before fixation - highlighting the method's sensitivity to ongoing selective processes. CONCLUSIONS: Furthermore, we emphasize the critical role of parameter tuning, balancing biological assumptions with methodological rigor. While broader applicability remains an important direction for future work, the present benchmarking is intentionally scoped to EaR experimental contexts.

Machine Learning↗
PubMed2001

[Potential functional differentiation of genome in the course of evolution and approaches to its study. II. Elucidation of diversity of phylogenetic lines].

It has been shown elsewhere (Chupov, 2001) that the branching of phylogenetical trunks goes by anisotomical way. Thus, in one of newly formed branches a possibility remains of a further evolutionary transformation, while taxa belonging to another branch sink into a prolonged evolutionary stasis. In the author's opinion, such a phenomenon is to be accompanied by distinctions in constitution of genetical cell devices of the taxa belonging to the branches with evolutionary contrasting potencies. In the article, an attempt is done to consider some other approaches relevant to this problem.

Evolution, Molecular↗
PubMed2004

A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium).

We report genetic maps for diploid (D) and tetraploid (AtDt) Gossypium genomes composed of sequence-tagged sites (STS) that foster structural, functional, and evolutionary genomic studies. The maps include, respectively, 2584 loci at 1.72-cM ( approximately 600 kb) intervals based on 2007 probes (AtDt) and 763 loci at 1.96-cM ( approximately 500 kb) intervals detected by 662 probes (D). Both diploid and tetraploid cottons exhibit negative crossover interference; i.e., double recombinants are unexpectedly abundant. We found no major structural changes between Dt and D chromosomes, but confirmed two reciprocal translocations between At chromosomes and several inversions. Concentrations of probes in corresponding regions of the various genomes may represent centromeres, while genome-specific concentrations may represent heterochromatin. Locus duplication patterns reveal all 13 expected homeologous chromosome sets and lend new support to the possibility that a more ancient polyploidization event may have predated the A-D divergence of 6-11 million years ago. Identification of SSRs within 312 RFLP sequences plus direct mapping of 124 SSRs and exploration for CAPS and SNPs illustrate the "portability" of these STS loci across populations and detection systems useful for marker-assisted improvement of the world's leading fiber crop. These data provide new insights into polyploid evolution and represent a foundation for assembly of a finished sequence of the cotton genome.

Chromosome Mapping↗
PubMed1993

Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse.

Gene constellations on several human chromosomes are interpreted as indications of large regional duplications that took place during evolution of the vertebrate genome. Four groups of paralogous chromosomal regions in man and the house mouse are suggested and are believed to be conserved remnants of the two or three rounds of tetraploidization that are likely to have occurred during evolution of the vertebrates. The phenomenon of differential silencing of genes is described. The importance of conservation of linkage of particular genes is discussed in relation to genetic regulation and cell differentiation.

Animals↗
PubMed1999

Local-scale repetitiveness in amino acid use in eukaryote protein sequences: a genomic factor in protein evolution.

We showed previously that the use of arginine versus lysine residues in eukaryote proteins is correlated positively with local GC content of the genome within approximately 50 residues. Cumulative analyses show that the tendency for self-clustering (or repetitive use) generally is the case for all types of amino acids except for certain hydrophobic types. The degree to which each of the amino acids is used recurrently is weak for ancient proteins (or protein domains), those that are conserved through both eukaryotes and prokaryotes, but strong for modern proteins, which are unique to organisms of particular phyla. These findings support the idea that repetitiveness occurs due to a propensity of genomic DNA to cause tandem genomic duplication. A protein sequence with high repetitiveness tends to be unique in the homology search, which may indicate the weaker constraints and, hence, more arbitrary use of amino acids. Simulation analyses suggest that tandem gene duplications on a very small scale (1 or 2 codons) is an important causal factor in maintaining repetitiveness in the presence of concomittant occurrence of substitutive point mutation. For yeast proteins, approximately 1.3 duplication events per 1,000 residues on average are likely to occur, whereas 10 events of substitution mutation occur. It also is suggested that duplication enhances the probability of occurrence of some peptide motifs, such as those found in zinc fingers and segments with extreme physicochemical characteristics, and, thus, that local repetitiveness is a genomic factor influencing the evolution of eukaryote proteins.

Amino Acid Motifs↗
PubMed2002

[Molecular evolution of tandem heterochromatic repeats in connection with their function in the genome of Drosophila melanogaster].

Molecular evolution and divergence of paralogous tandem heterochromatic repeats Stellate and Su(Ste) located on the X and Y chromosomes, respectively, are discussed. These repeats appear to emerge as a result of amplification of a unique autosomal euchromatic gene encoding the regulatory beta-subunit of the CK2 protein kinase. The autosomal gene and the clusters of heterochromatic repeats are transcribed in testes. A high level of the Stellate expression leads to partial male sterility and disturbed meiosis. The Stellate expression and its adverse effects are suppressed by homologous Su(Ste) repeats. In genome evolution, the open reading frames (ORF) of Stellate and Su(Ste) putative ancestor were maintained by translational selection. Then the coding Su(Ste) function had been damaged and switched to a new one related to antisense Su(Ste) transcription and suppression of the Stellate genes. Symmetrical (sense and antisense) Su(Ste) transcription causes the formation of a double-strand RNA, which by interference (selective switching off the homologous gene expression) suppresses the Stellate genes. The biological significance and the driving forces of evolution of the species-specific balanced interaction of Stellate and Su(Ste) repeats remain mysterious.

Amino Acid Sequence↗
PubMed1999

Genomic demography: a life-history analysis of transposable element evolution.

Retrotransposons are ubiquitous mobile genetic elements that have played a significant role in shaping eukaryotic genome evolution. The genome of the yeast Saccharomyces cerevisiae harbours five families of retrotransposons, Ty1-Ty5. With the publication of the S. cerevisiae genome sequence, for the first time a full genomic complement of retrotransposon sequences is available. Analysis of these sequences promises to yield insight into the nature of host--transposon coevolution. Evolutionary change in Ty elements depends on their replication and excision rates, which have been determined in the laboratory. Rates measured in the laboratory may differ from those that have operated over evolutionary time. Based on an analysis of sequence data for the Ty1, Ty2 and hybrid Ty1/2 families, we develop a novel 'genomic demography' model to estimate long-term transposition and excision rates and to estimate how long ago these elements entered the yeast genome. We find that rates of excision and transposition have averaged 7.2-8.7 x 10(-8) per generation over evolutionary time. Two separate models provide upper- and lower-bound estimates for the age of the system, suggesting that the first elements entered the genome between approximately 50 million and 250 million generations ago.

Evolution, Molecular↗
PubMed2025

Transposable elements create distinct genomic niches for effector evolution among Magnaporthe oryzae lineages.

BACKGROUND: Plant-pathogen interactions are characterized by evolutionary arms races. At the molecular level, fungal effectors can target important plant functions, while plants evolve to improve effector recognition. Rapid evolution in genes encoding effectors can be facilitated by transposable elements (TEs). In Magnaporthe oryzae, the causal agent of blast disease in several cereals and grasses, TEs play important roles in chromosomal evolution as well as the gain or loss of effector genes in host specialized lineages. However, a global understanding of TE dynamics driving effector evolution at population scale and across lineages is lacking. RESULTS: Here, we focus on 16 AVR effector loci assessed across a global sampling of 11 reference genomes and 447 newly generated draft genome assemblies from publicly available short-read sequencing data across all major M. oryzae lineages and outgroups. We classified each effector based on evidence for duplication, deletion and translocation processes among lineages. Next, we determined AVR gain and loss dynamics across lineages allowing for a broad categorization of effector dynamics. Each AVR was integrated in a distinct genomic niche determined by the TE activity profile contributing to the diversification at the locus. We quantified TE contributions to effector niches and found that TE identity helped diversify AVR loci. We used the large genomic dataset to recapitulate the evolution of the rice blast AVR1-CO39 locus. CONCLUSIONS: Taken together, our work demonstrates how TE dynamics are an integral component of M. oryzae effector evolution, likely facilitating escape from host recognition. In-depth tracking of effector loci is a valuable tool to predict the durability of host resistance.

Ascomycota↗
PubMed1998

Genomics: re-evaluation of translation machinery evolution.

Experiments based on genome sequence analysis have revealed unexpected complexity in the evolution of the translation apparatus, including concerted evolution of Gln-tRNA synthetase and Glu-tRNAGln amidotransferase, and a novel, class I Lys-tRNA synthetase shared by archaea and spirochaetes.

Amino Acyl-tRNA Synthetases↗
PubMed1990

Mitochondrial genome: defects, disease, and evolution.

Defects of mitochondrial function are often caused by defects of the mitochondrial genome. The hypothesis that defective organelles may spread through syncytial tissues as a result of a process of subcellular Darwinian selection is proposed. Tissues are likely to be involved in mitochondrial disease if they are syncytial, are derived from a few embryonic cells only, have little redundancy of function, and are subject to repeated metabolic stress. These effects, together with the random distribution of genetically heterogeneous mitochondria within the fertilised zygote, may account for the varied clinical pictures of mitochondrial disease. Evolution will have favoured the shift of mitochondrial DNA sequences to the nucleus, once the differentiation of tissues had created body compartments in which defective mitochondria could flourish to the detriment of the organism. This model of mitochondrial disease allows the generation of several predictions, testable using currently available laboratory techniques. Avenues of potential therapeutic value are indicated, including the avoidance of hypoglycaemia and the use of selective mitochondrial toxins.

Biological Evolution↗