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Results for “genome evolution”

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At least 19 recordsLinked to original sources

PubMed2005

Genome trees and the nature of genome evolution.

Genome trees are a means to capture the overwhelming amount of phylogenetic information that is present in genomes. Different formalisms have been introduced to reconstruct genome trees on the basis of various aspects of the genome. On the basis of these aspects, we separate genome trees into five classes: (a) alignment-free trees based on statistic properties of the genome, (b) gene content trees based on the presence and absence of genes, (c) trees based on chromosomal gene order, (d) trees based on average sequence similarity, and (e) phylogenomics-based genome trees. Despite their recent development, genome tree methods have already had some impact on the phylogenetic classification of bacterial species. However, their main impact so far has been on our understanding of the nature of genome evolution and the role of horizontal gene transfer therein. An ideal genome tree method should be capable of using all gene families, including those containing paralogs, in a phylogenomics framework capitalizing on existing methods in conventional phylogenetic reconstruction. We expect such sophisticated methods to help us resolve the branching order between the main bacterial phyla.

Evolution, Molecular↗

PubMed1999

Yeast genome evolution in the post-genome era.

The Saccharomyces cerevisiae genome sequence, augmented by new data on gene expression and function, continues to yield new findings about eukaryote genome evolution. Analysis of the duplicate gene pairs formed by whole-genome duplication indicates that selection for increased levels of gene expression was a significant factor determining which genes were retained as duplicates and which were returned to a single-copy state, possibly in addition to selection for novel gene functions. Proteome comparisons between worm and yeast show that genes for core metabolic processes are shared among eukaryotes and unchanging in function, while comparisons between different yeast species identify 'orphan' genes as the most rapidly evolving fraction of the proteome. Natural hybridisation among yeast species is frequent, but its long-term evolutionary significance is unknown.

Evolution, Molecular↗

PubMed2003

Innovation from reduction: gene loss, domain loss and sequence divergence in genome evolution.

Analyses of genome sequences have revealed a surprisingly variable distribution of genes, reflecting the generation of novel genes, lateral gene transfer and gene loss. The impact of gene loss on organisms has been difficult to examine, but the loss of protein coding genes, the loss of domains within proteins and the divergence of genes have made surprising contributions to the differences among organisms. This paper reviews surveys of gene loss and divergence in fungal and archaeal genomes that indicate suites of functionally related genes tend to undergo loss and divergence. Instances of fungal gene loss highlighted here suggest that specific cellular systems have changed, such as Ca 2+ biology in Saccharomyces cerevisiae and peroxisome function in Schizosaccharomyces pombe. Analyses of loss and divergence can provide specific predictions regarding protein-protein interactions, and the relationship between networks of protein interactions and loss may form a part of a parametric model of genome evolution.

Chromosome Mapping↗

PubMed2002

Plant genome evolution: lessons from comparative genomics at the DNA level.

Angiosperm genomes show tremendous variability in genome size and chromosome number. Nevertheless, comparative genetic mapping has revealed genome collinearity of closely related species. Sequence-based comparisons were used to assess the conservation of gene arrangements. Numerous small rearrangements, insertions/deletions, duplications, inversions and translocations have been detected. Importantly, comparative sequence analyses have unambiguously shown micro-collinearity of distantly related plant species. Duplications and subsequent gene loss have been identified as a particular important factor in the evolution of plant genomes.

Base Composition↗

PubMed1996

Genomic organization of purK and purE in Brevibacterium ammoniagenes ATCC 6872: purE locus provides a clue for genomic evolution.

From the genomic library of Brevibacterium ammoniagenes ATCC6872, the purE locus encoding 5'-phosphoribosyl-5-aminoimidazole (AIR) carboxylase (EC 4.1.1.21) was cloned and its nucleotide sequence was determined. From the sequence analysis, two distinct open reading frames (ORFs) in the sequence of the purE locus were identified as purK and purE genes (purK-purE). An in vivo translation experiment reconfirmed the purK and purE genes to be independent. The genomic organization in the purE locus of B. ammoniagenes is opposite to that of the bacteria Escherichia coli and Bacillus subtilis. However, it coincides with the fused genes (purKE) of higher organisms Saccharomyces cerevisiae, Schizosaccharomyces pombe and Vigna aconitifolia. This suggests that the purE locus might be an intermediate form for genomic evolution of bacteria to higher organisms.

Amino Acid Sequence↗

PubMed2004

Mobile elements: drivers of genome evolution.

Mobile elements within genomes have driven genome evolution in diverse ways. Particularly in plants and mammals, retrotransposons have accumulated to constitute a large fraction of the genome and have shaped both genes and the entire genome. Although the host can often control their numbers, massive expansions of retrotransposons have been tolerated during evolution. Now mobile elements are becoming useful tools for learning more about genome evolution and gene function.

Alu Elements↗

PubMed2001

Experimental genome evolution: large-scale genome rearrangements associated with resistance to replacement of a chromosomal restriction-modification gene complex.

Type II restriction enzymes are paired with modification enzymes that protect type II restriction sites from cleavage by methylating them. A plasmid carrying a type II restriction-modification gene complex is not easily replaced by an incompatible plasmid because loss of the former leads to cell death through chromosome cleavage. In the present work, we looked to see whether a chromosomally located restriction-modification gene complex could be replaced by a homologous stretch of DNA. We tried to replace the PaeR7I gene complex on the Escherichia coli chromosome by transducing a homologous stretch of PaeR7I-modified DNA. The replacement efficiency of the restriction-modification complex was lower than expected. Some of the resulting recombinant clones retained the recipient restriction-modification gene complex as well as the homologous DNA (donor allele), and slowly lost the donor allele in the absence of selection. Analysis of their genome-wide rearrangements by Southern hybridization, inverse polymerase chain reaction (iPCR) and sequence determination demonstrated the occurrence of unequal homologous recombination between copies of the transposon IS3. It was strongly suggested that multiple rounds of unequal IS3-IS3 recombination caused large-scale duplication and inversion of the chromosome, and that only one of the duplicated copies of the recipient PaeR7I was replaced.

Chromosomes, Bacterial↗

PubMed2005

A 21st century view of evolution: genome system architecture, repetitive DNA, and natural genetic engineering.

The last 50 years of molecular genetics have produced an abundance of new discoveries and data that make it useful to revisit some basic concepts and assumptions in our thinking about genomes and evolution. Chief among these observations are the complex modularity of genome organization, the biological ubiquity of mobile and repetitive DNA sequences, and the fundamental importance of DNA rearrangements in the evolution of sequenced genomes. This review will take a broad overview of these developments and suggest some new ways of thinking about genomes as sophisticated informatic storage systems and about evolution as a systems engineering process.

Animals↗

PubMed2006

Strict host-symbiont cospeciation and reductive genome evolution in insect gut bacteria.

Host-symbiont cospeciation and reductive genome evolution have been identified in obligate endocellular insect symbionts, but no such example has been identified from extracellular ones. Here we first report such a case in stinkbugs of the family Plataspidae, wherein a specific gut bacterium is vertically transmitted via "symbiont capsule." In all of the plataspid species, females produced symbiont capsules upon oviposition and their gut exhibited specialized traits for capsule production. Phylogenetic analysis showed that the plataspid symbionts constituted a distinct group in the gamma-Proteobacteria, whose sister group was the aphid obligate endocellular symbionts Buchnera. Removal of the symbionts resulted in retarded growth, mortality, and sterility of the insects. The host phylogeny perfectly agreed with the symbiont phylogeny, indicating strict host-symbiont cospeciation despite the extracellular association. The symbionts exhibited AT-biased nucleotide composition, accelerated molecular evolution, and reduced genome size, as has been observed in obligate endocellular insect symbionts. These findings suggest that not the endocellular conditions themselves but the population genetic attributes of the vertically transmitted symbionts are probably responsible for the peculiar genetic traits of these insect symbionts. We proposed the designation "Candidatus Ishikawaella capsulata" for the plataspid symbionts. The plataspid stinkbugs, wherein the host-symbiont associations can be easily manipulated, provide a novel system that enables experimental approaches to previously untouched aspects of the insect-microbe mutualism. Furthermore, comparative analyses of the sister groups, the endocellular Buchnera and the extracellular Ishikawaella, would lead to insights into how the different symbiotic lifestyles have affected their genomic evolution.

Animals↗

PubMed2005

Polyploidy and genome evolution in plants.

Genome doubling (polyploidy) has been and continues to be a pervasive force in plant evolution. Modern plant genomes harbor evidence of multiple rounds of past polyploidization events, often followed by massive silencing and elimination of duplicated genes. Recent studies have refined our inferences of the number and timing of polyploidy events and the impact of these events on genome structure. Many polyploids experience extensive and rapid genomic alterations, some arising with the onset of polyploidy. Survivorship of duplicated genes are differential across gene classes, with some duplicate genes more prone to retention than others. Recent theory is now supported by evidence showing that genes that are retained in duplicate typically diversify in function or undergo subfunctionalization. Polyploidy has extensive effects on gene expression, with gene silencing accompanying polyploid formation and continuing over evolutionary time.

Evolution, Molecular↗

PubMed1997

On some operations suggested by genome evolution.

Three operations involved in the genome evolution namely, inversion, transposition and duplication, are considered as operations on strings and languages. We show that, for any pair of these operations, there is a language family which is closed under one of the operations and not closed under the second one, however, under some mild conditions the closure of a language family under one of the operations implies that it also closed with respect to another one.

Alternative Splicing↗

PubMed2004

Lack of mismatch correction facilitates genome evolution in mycobacteria.

In silico genome sequence analyses suggested that mycobacteria are devoid of the highly conserved mutLS-based post-replicative mismatch repair system. Here, we present the first biological evidence for the lack of a classical mismatch repair function in mycobacteria. We found that frameshifts, but not general mutation rates are unusually high in Mycobacterium smegmatis. However, despite the absence of mismatch correction, M. smegmatis establishes a strong barrier to recombination between homeologous DNA sequences. We show that 10-12% of DNA sequence heterology restricts initiation of recombination but not extension of heteroduplex DNA intermediates. Together, the lack of mismatch correction and a high stringency of initiation of homologous recombination provide an adequate strategy for mycobacterial genome evolution, which occurs by gene duplication and divergent evolution.

Base Pair Mismatch↗

PubMed2006

Comparative genome maps of the pangolin, hedgehog, sloth, anteater and human revealed by cross-species chromosome painting: further insight into the ancestral karyotype and genome evolution of eutherian mammals.

To better understand the evolution of genome organization of eutherian mammals, comparative maps based on chromosome painting have been constructed between human and representative species of three eutherian orders: Xenarthra, Pholidota, and Eulipotyphla, as well as between representative species of the Carnivora and Pholidota. These maps demonstrate the conservation of such syntenic segment associations as HSA3/21, 4/8, 7/16, 12/22, 14/15 and 16/19 in Eulipotyphla, Pholidota and Xenarthra and thus further consolidate the notion that they form part of the ancestral karyotype of the eutherian mammals. Our study has revealed many potential ancestral syntenic associations of human chromosomal segments that serve to link the families as well as orders within the major superordinial eutherian clades defined by molecular markers. The HSA2/8 and 7/10 associations could be the cytogenetic signatures that unite the Xenarthrans, while the HSA1/19p could be a putative signature that links the Afrotheria and Xenarthra. But caution is required in the interpretation of apparently shared syntenic associations as detailed analyses also show examples of apparent convergent evolution that differ in breakpoints and extent of the involved segments.

Animals↗

PubMed2004

Genome evolution: the dynamics of static genomes.

A random survey of a microsporidian genome has revealed some striking features. Although the genomes of microsporidians are among the smallest known for eukaryotes, their organisation appears to be well conserved.

Animals↗

PubMed1998

Gene silencing in plants: relevance for genome evolution and the acquisition of genomic methylation patterns.

Transgenes often become silenced in plants because of repressive influences exerted by flanking plant DNA and/or because of interactions among multiple copies of closely linked transgenes. Repeated transgenes on different chromosomes can also interact in a way that leads to silencing and methylation, suggesting a previously unrecognized ability of unlinked homologous sequences to cross-talk in complex genomes. Non-Mendelian inheritance is a frequent consequence of these interactions because the silenced genes do not fully reactivate or lose methylation after segregating in progeny. Several examples of gene silencing in plants appear to reflect the action of genome defence system that methylates and inactivates foreign or invasive sequences such as transgenes and transposable elements. Because certain types of transposable elements are embedded in regulatory regions of plant genes and have become greatly amplified in plant genomes, they could contribute substantially to normal gene expression and to the generation of genomic methylation patterns. Polyploidy, which has been a major force in plant and vertebrate evolution, might encourage proliferation of transposable elements because genes in polyploids are duplicated and hence less susceptible to the consequences of insertional mutagenesis. Accordingly, the appearance of genome-wide methylation has often coincided with episodes of polyploidization.

DNA Methylation↗

PubMed1986

Compositional constraints and genome evolution.

Nucleotide sequences of all genomes are subject to compositional constraints that affect, to about the same extent, both coding and noncoding sequences; influence not only the structure and function of the genome, but also those of transcripts and proteins; are the result of environmental pressures; and largely control the fixation of mutations. These findings indicate that noncoding sequences are associated with biological functions; that the organismal phenotype comprises two components, the classical phenotype, corresponding to the "gene products," and a "genome phenotype," which is defined by the compositional constraints; and that natural selection plays a more important role in genome evolution than do random events.

Base Composition↗

PubMed2003

Simple stochastic birth and death models of genome evolution: was there enough time for us to evolve?

MOTIVATION: The distributions of many genome-associated quantities, including the membership of paralogous gene families can be approximated with power laws. We are interested in developing mathematical models of genome evolution that adequately account for the shape of these distributions and describe the evolutionary dynamics of their formation. RESULTS: We show that simple stochastic models of genome evolution lead to power-law asymptotics of protein domain family size distribution. These models, called Birth, Death and Innovation Models (BDIM), represent a special class of balanced birth-and-death processes, in which domain duplication and deletion rates are asymptotically equal up to the second order. The simplest, linear BDIM shows an excellent fit to the observed distributions of domain family size in diverse prokaryotic and eukaryotic genomes. However, the stochastic version of the linear BDIM explored here predicts that the actual size of large paralogous families is reached on an unrealistically long timescale. We show that introduction of non-linearity, which might be interpreted as interaction of a particular order between individual family members, allows the model to achieve genome evolution rates that are much better compatible with the current estimates of the rates of individual duplication/loss events.

Computer Simulation↗

PubMed2004

Genome evolution in yeasts.

Identifying the mechanisms of eukaryotic genome evolution by comparative genomics is often complicated by the multiplicity of events that have taken place throughout the history of individual lineages, leaving only distorted and superimposed traces in the genome of each living organism. The hemiascomycete yeasts, with their compact genomes, similar lifestyle and distinct sexual and physiological properties, provide a unique opportunity to explore such mechanisms. We present here the complete, assembled genome sequences of four yeast species, selected to represent a broad evolutionary range within a single eukaryotic phylum, that after analysis proved to be molecularly as diverse as the entire phylum of chordates. A total of approximately 24,200 novel genes were identified, the translation products of which were classified together with Saccharomyces cerevisiae proteins into about 4,700 families, forming the basis for interspecific comparisons. Analysis of chromosome maps and genome redundancies reveal that the different yeast lineages have evolved through a marked interplay between several distinct molecular mechanisms, including tandem gene repeat formation, segmental duplication, a massive genome duplication and extensive gene loss.

Chromosomes, Fungal↗