Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Genome evolution”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,693 records · Page 94Linked to original sources
PubMed1993

Anchored reference loci for comparative genome mapping in mammals.

Recent advances in gene mapping technologies have led to increased emphasis in developing representative genetic maps for several species, particularly domestic plants and animals. These maps are being compiled with two distinct goals: to provide a resource for genetic analysis, and to help dissect the evolution of genome organization by comparing linkage relationships of homologous genes. We propose here a list of 321 reference anchor loci suitable for comparative gene mapping in mammals and other vertebrate classes. We selected cloned mouse and human functional genes spaced an average of 5-10 centiMorgans throughout their respective genomes. We also attempted to include loci that are evolutionarily conserved and represented in comparative gene maps in other mammalian orders, particularly cattle and the domestic cat. We believe that the map may provide the basis for a unified approach to comparative analysis of mammalian species genomes.

Animals↗
PubMed2025

Precision projections of the delay of resistance mutations in non-small cell lung cancer via suppression of APOBEC.

Genomic instability driven by stress-response-dependent mutagenesis is a key factor in cancer progression. Tyrosine kinase inhibitor therapy, a common treatment for non-small cell lung cancer, induces mutations that can facilitate the evolution of drug resistance and therapeutic failure. Here we quantified the contribution of APOBEC to mutational signatures in non-small cell lung cancer patients undergoing TKI therapy. By analyzing tumor sequence data to infer gene-specific and patient-specific trinucleotide mutation rates, we projected the potential delay of resistance obtained by suppression of APOBEC mutation. Our data-driven analysis indicates that inhibition of APOBEC activity would substantially extend therapeutic efficacy, with the degree of benefit varying based on patient-specific APOBEC mutagenesis levels. Personalized therapeutic strategies that target APOBEC offer promise for the enhancement of TKI treatment efficacy by delaying the evolution of drug resistance in lung cancer. Development of clinically safe inhibitors for use in combination with tyrosine kinase inhibitors could significantly limit tumor genetic variation and improve outcomes for non-small cell lung cancer patients.

Humans↗
PubMed1996

Models of parasite virulence.

Several evolutionary processes influence virulence, the amount of damage a parasite causes to its host. For example, parasites are favored to exploit their hosts prudently to prolong infection and avoid killing the host. Parasites also need to use some host resources to reproduce and transmit infections to new hosts. Thus parasites face a tradeoff between prudent exploitation and rapid reproduction-a life history tradeoff between longevity and fecundity. Other tradeoffs among components of parasite fitness also influence virulence. For example, competition among parasite genotypes favors rapid growth to achieve greater relative success within the host. Rapid growth may, however, lower the total productivity of the local group by overexploiting the host, which is a potentially renewable food supply. This is a problem of kin selection and group selection. I summarize models of parasite virulence with the theoretical tools of life history analysis, kin selection, and epidemiology. I then apply the theory to recent empirical studies and models of virulence. These applications, to nematodes, to the extreme virulence of hospital epidemics, and to bacterial meningitis, show the power of simple life history theory to highlight interesting questions and to provide a rich array of hypotheses. These examples also show the kinds of conceptual mistakes that commonly arise when only a few components of parasite fitness are analysed in isolation. The last part of the article connects standard models of parasite virulence to diverse topics, such as the virulence of bacterial plasmids, the evolution of genomes, and the processes that influenced conflict and cooperation among the earliest replicators near the origin of life.

Animals↗
PubMed2001

Evolution, language and analogy in functional genomics.

Almost a century ago, Wittgenstein pointed out that theory in science is intricately connected to language. This connection is not a frequent topic in the genomics literature. But a case can be made that functional genomics is today hindered by the paradoxes that Wittgenstein identified. If this is true, until these paradoxes are recognized and addressed, functional genomics will continue to be limited in its ability to extrapolate information from genomic sequences.

Amino Acid Sequence↗
PubMed1993

Origins of species: acquired genomes and individuality.

Entire genomes with their accompanying protein synthetic systems are transferred throughout the biosphere primarily as bacteria and protists which become symbionts as they irreversibly integrate into pre-existing organisms to form more complex individuals. Individualization is stabilized by simultaneous transmission of once-separate heterologous genetic systems. The origin of new species is hypothesized to correlate with the acquisition, integration and subsequent inheritance of such acquired microbial genomes. These processes were recognized by Mereschkovsky ("Symbiogenesis" in Russian, 1909) and by Wallin ("Symbionticism", see p. 181, this issue).

Animals↗
PubMedDate not supplied

Meeting our friend, the genome.

(1) Encounter with the genome. (2) Difficulties in the path. (3) Legal and ethical implications. (4) Patenting genes. (5) The genome and evolution. (6) An adjunct to medicine or a new world? (7) Forbidden territory or the next step for humanity? (8) Informed decisions.

Genetics↗
PubMed2006

Male killers and the origins of paternal genome elimination.

The haploidizing male killer hypothesis suggests an evolutionary origin for paternal genome elimination (PGE) that is consistent with the ecological correlates of ancestral haplodiploid insect clades. We make use of population genetics models to test the logic and assumptions of this hypothesis with particular emphasis on the co-evolution between bacteria and host. We derive simple invasion conditions for rare modifiers of bacteria transmission and rare modifiers of host survivorship after haploidization. We also study the evolutionary dynamics of both these modifiers. We conclude that PGE shows evolutionary genetic stability and present a comprehensive analysis of the probability that such genetic system evolves due to the action of cytoplasmic genes.

Animals↗
PubMed2003

Dividing the child.

The evolution of genomic imprinting is viewed as a problem of economic optimization that is analyzed using the tools of evolutionary game theory. We specifically consider genetic conflicts over the allocation of maternal resources between present and future offspring. Five sets of genes, with the same interests within sets but distinct interests between sets, are considered as agents: maternal alleles (Mater), paternal alleles (Pater), unimprinted offspring alleles (Filius), and imprinted offspring alleles of maternal and paternal origin (Matris and Patris). Fitness functions are derived for each agent and the parameter space in which there is conflict defined. Three potential conflicts are considered: between mother and offspring (Mater v.s. Filius); between alleles of maternal and paternal origin within offspring (Matris v.s. Patris) and between mothers and the paternally derived alleles of offspring (Mater v.s. Patris).

Alleles↗
PubMed2002

Yeast genomic expression studies using DNA microarrays.

The exploration and characterization of yeast genomic expression programs is providing a wealth of information about yeast biology, as well as other organisms. The intriguing biology of yeast species invites characterization of genomic expression patterns to illuminate the details of cellular physiology. In addition to its value as an interesting organism, yeast maintains its role as an excellent model in which to characterize genomic expression programs. Microarray studies are quickly spreading to plant, animal, and microbial organisms that remain in the early stages of characterization. The extensive knowledge of yeast biology, as well as the relative ease with which yeast studies can be performed and controlled, facilitates interpretation of the genomic expression data. Importantly, existing information about yeast biology, including functional annotations for each gene, is captured and efficiently presented in databases such as the Saccharomyces Genome Database (SGD), the Munich Information Center Yeast Genome Database (MIPS), the Yeast and Pombe Protein Databases (YPD and PPD, respectively), and others. A number of databases also allow the exploration of published genomic expression studies, including the "Expression Connection" at SGD and the Microarray Global Viewer (yMGV) organized by Marc et al. Consulting these databases to retrieve known details about gene function and regulation vastly facilitates interpretation of the genomic expression data, allowing biological hypotheses to be formulated and tested. These hypotheses can be applied to other organisms that may execute genomic expression programs similar to those seen in yeast. Furthermore, as more genomic expression studies in multiple organisms emerge, large-scale data comparisons can be conducted, within and across organisms. Incorporating the results of yeast studies into such comparisons is certain to increase our understanding about the function, regulation, and evolution of genomic expression programs.

Carbocyanines↗
PubMed2000

The skeletal muscle alpha-actin gene of channel catfish (Ictalurus punctatus) and its association with piscine specific SINE elements.

The alpha-actin gene of channel catfish (Ictalurus punctatus) was cloned and sequenced. The gene has a similar organization and exhibited a high level of sequence similarity to those from other vertebrate animals. The upstream region of the alpha-actin gene included a TATA box, a CAAT box, three E-boxes, and a CArG box. Nested deletion segments containing these transcriptional motifs were fused to the reporter gene chloramphenicol acetyl transferase (CAT). Transfection of the clones into C2C12 cells indicated that all these motifs are required for transcriptional activities. The channel catfish alpha-actin gene is associated with two distinct short interspersed repetitive elements (SINEs). The first SINE element showed high levels of sequence similarity to the zebrafish Mermaid element, while the second SINE element is not similar to the Mermaid element except for an 8bp sequence CCCCGTGC suggesting their evolutionary linkage. However, the second SINE element appeared to co-exist with the Mermaid element in most cases and therefore was designated as the Merman element. Approximately 9000 copies and 1200 copies of the Mermaid and Merman elements exist per haploid channel catfish genome, respectively. BLAST searches indicated that both the Mermaid and the Merman elements were frequently associated with gene sequences, mostly those of aquatic animals, suggesting their evolutionary origin in association with aquatic organisms and their function in shaping the evolution of genomes in aquatic animals.

Actins↗
PubMed1997

Before crossing over: the advantages of eukaryotic sex in genomes lacking chiasmatic recombination.

Non-recombining populations should suffer from four classic population genetic disadvantages: (1) they cannot reverse Muller's Ratchet, the accumulation of deleterious mutations caused by genetic drift and mutation; (2) whenever the fix a favourable mutation they lose all unlinked favourable variants; (3) they tend to lose favourable mutations that are linked to deleterious mutations; and (4) their genetic loads can be quite high when deleterious mutations have synergistic effects. It is commonly assumed that inter-chromosomal recombination (independent assortment) can counter these phenomena, but this has been studied only for the genetic load case. In contrast, many studies have shown that recombination via crossing over can counter these phenomena. Here we first show that segregation alone can strongly decelerate Muller's Ratchet in diploids, i.e. that recombination is not the only way to do so. We then show that inter-chromosomal recombination can indeed deal with phenomena (1) to (3) above very effectively if the genome consists of a moderate number of chromosomes. Therefore, if the above advantages of genetic recombination played a large role in the initial success of eukaryotic sex, the crucial moment in the origin of sex might have been the evolution of inter-chromosomal recombination, i.e. the evolution of genome segmentation, segregation, and syngamy. Crossing over might have become established as a major recombinational device only later, eliminating the disadvantages of extensively segmented genomes.

Crossing Over, Genetic↗
PubMed2006

Sexual conflict and the alternation of haploid and diploid generations.

Land plants possess a multicellular diploid stage (sporophyte) that begins development while attached to a multicellular haploid progenitor (gametophyte). Although the closest algal relatives of land plants lack a multicellular sporophyte, they do produce a zygote that grows while attached to the maternal gametophyte. The diploid offspring shares one haploid set of genes with the haploid mother that supplies it with resources and a paternal haploid complement that is not shared with the mother. Sexual conflict can arise within the diploid offspring because the offspring's maternal genome will be transmitted in its entirety to all other sexual and asexual offspring that the mother may produce, but the offspring's paternally derived genes may be absent from these other offspring. Thus, the selective forces favouring the evolution of genomic imprinting may have been present from the origin of modern land plants. In bryophytes, where gametophytes are long-lived and capable of multiple bouts of asexual and sexual reproduction, we predict strong sexual conflict over allocation to sporophytes. Female gametophytes of pteridophytes produce a single sporophyte and often lack means of asexual reproduction. Therefore, sexual conflict is predicted to be attenuated. Finally, we explore similarities among models of mate choice, offspring choice and segregation distortion.

Bryophyta↗
PubMed2005

Marsupials and monotremes sort genome treasures from junk.

A recent landmark paper demonstrates the unique contribution of marsupials and monotremes to comparative genome analysis, filling an evolutionary gap between the eutherian mammals (including humans) and more distant vertebrate species.

Animals↗
PubMed2006

Viruses of the Archaea: a unifying view.

DNA viruses of the Archaea have highly diverse and often exceptionally complex morphotypes. Many have been isolated from geothermally heated hot environments, raising intriguing questions about their origins, and contradicting the widespread notion of limited biodiversity in extreme environments. Here, we provide a unifying view on archaeal viruses, and present them as a particular assemblage that is fundamentally different in morphotype and genome from the DNA viruses of the other two domains of life, the Bacteria and Eukarya.

Archaea↗
PubMed1988

Mammalian homeobox-containing genes: genome organization, structure, expression and evolution.

Mammalian homeo box-containing genes have been isolated by their sequence similarity to Drosophila homeotic selector genes. About 20 murine homeo box genes have been identified to date and their expression and structural organization has been described in detail. Most homeo box gene loci are organized in at least three major gene clusters in the mouse and human genome. The structure of homeo box genes within these clusters is very similar and in this paper the murine Hox-2.2 gene will be discussed as an example. Homeo box genes are expressed in region-specific patterns during different stages of vertebrate development and almost all mammalian homeo box genes are expressed in the central nervous system (CNS) of the developing embryo. Within the developing CNS of mouse embryos the anterior boundaries of expression are specific for each gene. Comparisons of nucleotide and amino acid sequences as well as the analysis of the structural organization of murine and human homeo box genes reveal strong paralogous relationships between genes in different clusters. These findings suggest that the homeo box gene clusters evolved in two steps. First, an ancestral gene cluster was created by duplications of individual genes along one linkage group and in a subsequent step duplications of the ancestral gene complex gave rise to the three (or possibly four) gene clusters observed in mouse and human to date. The possibility of the homeo box genes representing a functional array of genetic switches will be discussed.

Amino Acid Sequence↗
PubMed1994

Chimeric evolution of the 2-microns genome in Saccharomyces cerevisiae.

We compared the nucleotide substitution pattern over the entire genome of two unique variants of the 6,300-bp selfish DNA (2 microns) plasmid in Saccharomyces cerevisiae. The DNA sequence of the left-unique region is identical among 2-microns variants, while the right-unique region shows substantial divergence. This chimeric pattern cannot be explained by neutral or Darwinian selection models. We propose that horizontal transmission of the 2-microns plasmid coupled with a directed, polarized gene conversion maintains the DNA sequence of the left-unique region, whereas the right-unique region is subject to random drift and Darwinian selection.

Base Sequence↗
PubMed2005

Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes.

Sequencing and comparative analyses of genomes from multiple vertebrates are providing insights about the genetic basis for biological diversity. To date, these efforts largely have focused on eutherian mammals, chicken, and fish. In this article, we describe the generation and study of genomic sequences from noneutherian mammals, a group of species occupying unusual phylogenetic positions. A large sequence data set (totaling >5 Mb) was generated for the same orthologous region in three marsupial (North American opossum, South American opossum, and Australian tammar wallaby) and one monotreme (platypus) genomes. These ancient mammalian genomes are characterized by unusual architectural features with respect to G + C and repeat content, as well as compression relative to human. Approximately 14% and 34% of the human sequence forms alignments with the orthologous sequence from platypus and the marsupials, respectively; these numbers are distinctly lower than that observed with nonprimate eutherian mammals (45-70%). The alignable sequences between human and each marsupial species are not completely overlapping (only 80% common to all three species) nor are the platypus-alignable sequences completely contained within the marsupial-alignable sequences. Phylogenetic analysis of synonymous coding positions reveals that platypus has a notably long branch length, with the human-platypus substitution rate being on average 55% greater than that seen with human-marsupial pairs. Finally, analyses of the major mammalian lineages reveal distinct patterns with respect to the common presence of evolutionarily conserved vertebrate sequences. Our results confirm that genomic sequence from noneutherian mammals can contribute uniquely to unraveling the functional and evolutionary histories of the mammalian genome.

Animals↗