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PubMed2004

Recent developments in computational approaches for uncovering genomic homology.

Identifying genomic homology within and between genomes is essential when studying genome evolution. In the past years, different computational techniques have been developed to detect homology even when the actual similarity between homologous segments is low. Depending on the strategy used, these methods search for pairs of chromosomal segments between which either both gene content and order are conserved or gene content only. However, due to fact that, after their divergence, homologous segments can lose a different set of genes, these methods still often fail to detect genomic homology. Recently, more advanced approaches have been developed that can combine gene order and content information of multiple genomic segments.

Animals↗
PubMed2000

Three-dimensional structure of the Tn5 synaptic complex transposition intermediate.

Genomic evolution has been profoundly influenced by DNA transposition, a process whereby defined DNA segments move freely about the genome. Transposition is mediated by transposases, and similar events are catalyzed by retroviral integrases such as human immunodeficiency virus-1 (HIV-1) integrase. Understanding how these proteins interact with DNA is central to understanding the molecular basis of transposition. We report the three-dimensional structure of prokaryotic Tn5 transposase complexed with Tn5 transposon end DNA determined to 2.3 angstrom resolution. The molecular assembly is dimeric, where each double-stranded DNA molecule is bound by both protein subunits, orienting the transposon ends into the active sites. This structure provides a molecular framework for understanding many aspects of transposition, including the binding of transposon end DNA by one subunit and cleavage by a second, cleavage of two strands of DNA by a single active site via a hairpin intermediate, and strand transfer into target DNA.

Amino Acid Motifs↗
PubMed1995

Wide Distribution of Mitochondrial Genome Rearrangements in Wild Strains of the Cultivated Basidiomycete Agrocybe aegerita.

We used restriction fragment length polymorphisms to examine mitochondrial genome rearrangements in 36 wild strains of the cultivated basidiomycete Agrocybe aegerita, collected from widely distributed locations in Europe. We identified two polymorphic regions within the mitochondrial DNA which varied independently: one carrying the Cox II coding sequence and the other carrying the Cox I, ATP6, and ATP8 coding sequences. Two types of mutations were responsible for the restriction fragment length polymorphisms that we observed and, accordingly, were involved in the A. aegerita mitochondrial genome evolution: (i) point mutations, which resulted in strain-specific mitochondrial markers, and (ii) length mutations due to genome rearrangements, such as deletions, insertions, or duplications. Within each polymorphic region, the length differences defined only two mitochondrial types, suggesting that these length mutations were not randomly generated but resulted from a precise rearrangement mechanism. For each of the two polymorphic regions, the two molecular types were distributed among the 36 strains without obvious correlation with their geographic origin. On the basis of these two polymorphisms, it is possible to define four mitochondrial haplotypes. The four mitochondrial haplotypes could be the result of intermolecular recombination between allelic forms present in the population long enough to reach linkage equilibrium. All of the 36 dikaryotic strains contained only a single mitochondrial type, confirming the previously described mitochondrial sorting out after cytoplasmic mixing in basidiomycetes.

Journal Article↗
PubMed2005

Demonstration of cotranscription and 1-methyl-3-nitroso-nitroguanidine induction of a 30-gene operon of Borrelia burgdorferi: evidence that the 32-kilobase circular plasmids are prophages.

The Borrelia genome is comprised of linear and circular elements, including a group of 32-kb circular plasmids (cp32s). Earlier analyses identified a bacteriophage, varphiBB-1, that may package cp32s, suggesting that these plasmids are prophages. cp32-8, cp32-9, and cp32-1 (plasmids L, N, and P, respectively) encode virulence factors such as the factor H binding, OspE proteins (BBL39, BBN38, and BBP38). Here the expression patterns of cp32-8 open reading frames (ORFs) in in vitro-cultivated 1-methyl-3-nitroso-nitroguanidine (MNNG)-treated and untreated spirochetes and during infection were assessed. ORFs BBL42 through BBL28, which encode several bacteriophage protein homologs, were found to be cotranscribed and expression was upregulated by MNNG. Immunoblotting revealed that MNNG-induced transcription led to increased protein production. The expression of several genes that reside outside of the BBL42-BBL28 operon was not affected by MNNG. Some of these genes, including OspE (BBL39), appear to represent morons. Real-time reverse transcription-PCR of spirochetes in mouse tissue revealed that although the phage operon was not induced during infection, transcription of BBL23 (previously designated BlyA), a putative holin, was upregulated. This observation indicates that some genes within the operon can be independently transcribed from internal promoters. Additional transcriptional analyses of the operon identified multiple transcriptional start sites and provided evidence for the expression of a homologous operon from other cp32s. The data support the hypothesis put forth by C. Eggers and D. S. Samuels (J. Bacteriol. 181:7308-7313, 1999) that the cp32s are prophages, a finding with broad implications for our understanding of Borrelia pathogenesis and Borrelia genome evolution.

Animals↗
PubMed2001

Escherichia coli and Salmonella 2000: the view from here.

Five years after the publication of the second edition of the reference book Escherichia coli and Salmonella: Cellular and Molecular Biology, and on the eve of launching a successor venture, the editors and colleagues examine where we stand in our quest for an understanding of these organisms. The main areas selected for this brief inquiry are genomics, evolution, molecular multifunctionality, functional backups, regulation of gene expression, cell biology, sensing of the environment, and ecology.

Biological Evolution↗
PubMed2005

Transposable elements donate lineage-specific regulatory sequences to host genomes.

The evolutionary implications of transposable element (TE) influences on gene regulation are explored here. An historical perspective is presented to underscore the importance of TE influences on gene regulation with respect to both the discovery of TEs and the early conceptualization of their potential impact on host genome evolution. Evidence that points to a role for TEs in host gene regulation is reviewed, and comparisons between genome sequences are used to demonstrate the fact that TEs are particularly lineage-specific components of their host genomes. Consistent with these two properties of TEs, regulatory effects and evolutionary specificity, human-mouse genome wide sequence comparisons reveal that the regulatory sequences that are contributed by TEs are exceptionally lineage specific. This suggests a particular mechanism by which TEs may drive the diversification of gene regulation between evolutionary lineages.

Animals↗
PubMed2006

Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network.

BACKGROUND: While gene duplication is known to be one of the most common mechanisms of genome evolution, the fates of genes after duplication are still being debated. In particular, it is presently unknown whether most duplicate genes preserve (or subdivide) the functions of the parental gene or acquire new functions. One aspect of gene function, that is the expression profile in gene coexpression network, has been largely unexplored for duplicate genes. RESULTS: Here we build a human gene coexpression network using human tissue-specific microarray data and investigate the divergence of duplicate genes in it. The topology of this network is scale-free. Interestingly, our analysis indicates that duplicate genes rapidly lose shared coexpressed partners: after approximately 50 million years since duplication, the two duplicate genes in a pair have only slightly higher number of shared partners as compared with two random singletons. We also show that duplicate gene pairs quickly acquire new coexpressed partners: the average number of partners for a duplicate gene pair is significantly greater than that for a singleton (the latter number can be used as a proxy of the number of partners for a parental singleton gene before duplication). The divergence in gene expression between two duplicates in a pair occurs asymmetrically: one gene usually has more partners than the other one. The network is resilient to both random and degree-based in silico removal of either singletons or duplicate genes. In contrast, the network is especially vulnerable to the removal of highly connected genes when duplicate genes and singletons are considered together. CONCLUSION: Duplicate genes rapidly diverge in their expression profiles in the network and play similar role in maintaining the network robustness as compared with singletons.

Chromosome Mapping↗
PubMed1999

Some remarks on the female and male Keimbahn in the light of evolution and history.

From the existence of two types of cells for reproduction-the female and male germ cells (GCs)-and by recombination of the genome, evolution proceeded dramatically. Unicellular and multicellular plants frequently are characterized by a sequence of haploid and diploid phases, or generations, with gametes and spores as reproductive cells. Isogamy, anisogamy, and oogamy can be distinguished depending on the GCs that correspond, differ in size, or impose as egg cell and sperm cell. In protozoans, too, species are found in which GCs differ clearly from each other. In the female lineage of angiosperms, a "Keimbahn chain" consisting of five successive germ line cells can be observed. Oogenesis and spermatogenesis are complete in coelenterates and similar in mammals. However, the controlling mechanisms are by far more complex in the latter. This means that the balance of hormonal and vegetative nervous influences (stimulation, inhibition) on gametogenesis is not primarily orientated on the germ line cells themselves, but mostly on the structural and functional situation of the gonads and the individual carriers. This becomes particularly evident in insects, where gametogenesis, on the one side, depends on the development of the rest of the organism but on the other side represents an independent developmental process. The point at which germ line cells and somatic cells separate correlates more or less with the degree of phylogenetic development. In worms, insects, and up to the anurans, a part of the cytoplasm, the so-called germ plasma, is separated for the development of GCs during oogenesis (preformistic development). However, in urodeles, reptiles, birds, and mammals, GCs and somatic cells cannot be distinguished before gastrulation (epigenetic development). In various species (e.g., in some oligochaetes and snails), there exist "double spermatogenic lines." In mammals (probably in other vertebrates and perhaps in various phyla of animals, too), the female Keimbahn is provided with only one proliferation system. The male gametogenesis is equipped with two systems: the first corresponds to the female germ line, the second is responsible for the immense number of gametes produced in the mature testes. In mammals the message to become male lies on the Y-chromosome (on its short arm in man and mouse) and was identified as the gene SRY in human and Sry in mouse. The fertility genes that are responsible for an uninterrupted spermatogenesis, up to fertilizing spermatozoa, are sitting on the long arm of the human Y-chromosome. J. Exp. Zool. (Mol. Dev. Evol.) 285:197-214, 1999.

Animals↗
PubMed2004

Prevalence of interspecific hybrids amongst asexual fungal endophytes of grasses.

Epichloë endophytes are fungal symbionts of grasses that span a continuum including asexual mutualists that are vertically transmitted, obligately sexual pathogens that are horizontally transmitted, and mixed-strategy symbionts with both mutualistic and pathogenic capabilities. Here we show that processes of genome evolution differ markedly for the different symbiont types. Genetic and phylogenetic analysis was conducted of a broad taxonomic, ecological and geographical sample of sexual and asexual isolates, in which were identified and sequenced alleles of genes for beta-tubulin (tub2) and translation elongation factor 1-alpha (tef1), and microsatellite alleles were identified by length polymorphisms. The majority of asexual isolates had two or three alleles of most loci, but every sexual isolate had only single alleles for each locus. Phylogenetic analysis of tub2 and tef1 indicated that in all instances of multiple alleles in an isolate, the alleles were derived from different sexual species. It is concluded that, whereas horizontally transmissible species had haploid genomes and speciation occurred cladistically, most of the strictly seedborne mutualists were interspecific hybrids with heteroploid (aneuploid or polyploid) genomes. Furthermore, the phylogenetic evidence indicated that, in at least some instances, hybridization followed rather than caused evolution of the strictly seedborne habit. Therefore, the abundance of hybrid species among grass endophytes, and their prevalence in many host populations suggests a selective advantage of hybridization for the mutualistic endophytes.

Base Sequence↗
PubMed2003

Genome rearrangements in mammalian evolution: lessons from human and mouse genomes.

Although analysis of genome rearrangements was pioneered by Dobzhansky and Sturtevant 65 years ago, we still know very little about the rearrangement events that produced the existing varieties of genomic architectures. The genomic sequences of human and mouse provide evidence for a larger number of rearrangements than previously thought and shed some light on previously unknown features of mammalian evolution. In particular, they reveal that a large number of microrearrangements is required to explain the differences in draft human and mouse sequences. Here we describe a new algorithm for constructing synteny blocks, study arrangements of synteny blocks in human and mouse, derive a most parsimonious human-mouse rearrangement scenario, and provide evidence that intrachromosomal rearrangements are more frequent than interchromosomal rearrangements. Our analysis is based on the human-mouse breakpoint graph, which reveals related breakpoints and allows one to find a most parsimonious scenario. Because these graphs provide important insights into rearrangement scenarios, we introduce a new visualization tool that allows one to view breakpoint graphs superimposed with genomic dot-plots.

Algorithms↗
PubMed1998

Rapid amplification of a retrotransposon subfamily is evolving the mouse genome.

Retrotransposition affects genome structure by increasing repetition and producing insertional mutations. Dispersion of the retrotransposon L1 throughout mammalian genomes suggests that L1 activity might be an important evolutionary force. Here we report that L1 retrotransposition contributes to rapid genome evolution in the mouse, because a number of L1 sequences from the T(F) subfamily are retrotransposition competent. We show that the T(F) subfamily is large, young and expanding, containing approximately 4,800 full-length members in strain 129. Eleven randomly isolated, full-length T(F) elements averaged 99.8% sequence identity to each other, and seven of these retrotransposed in cultured cells. Thus, we estimate that the mouse genome contains approximately 3,000 active T(F) elements, 75 times the estimated number of active human L1s. Moreover, as T(F) elements are polymorphic among closely related mice, they have retrotransposed recently, implying rapid amplification of the subfamily to yield genomes with different patterns of interspersed repetition. Our data show that mice and humans differ considerably in the number of active L1s, and probably differ in the contribution of retrotransposition to ongoing sequence evolution.

5' Untranslated Regions↗
PubMed2003

Neutral effect of recombination on base composition in Drosophila.

Recombination is thought to have various evolutionary effects on genome evolution. In this study, we investigated the relationship between the base composition and recombination rate in the Drosophila melanogaster genome. Because of a current debate about the accuracy of the estimates of recombination rate in Drosophila, we used eight different measures of recombination rate from recent work. We confirmed that the G + C content of large introns and flanking regions is positively correlated with recombination rate, suggesting that recombination has a neutral effect on base composition in Drosophila. We also confirmed that this neutral effect of recombination is the main determinant of the correlation between synonymous codon usage bias and recombination rate in Drosophila.

Animals↗
PubMed2006

Rate and polarity of gene fusion and fission in Oryza sativa and Arabidopsis thaliana.

Eukaryotic gene fusion and fission events are mechanistically more complicated than in prokaryotes, and their quantitative contributions to genome evolution are still poorly understood. We have identified all differentially composite or split genes in 2 fully sequenced plant genomes, Oryza sativa and Arabidopsis thaliana. Out of 10,172 orthologous gene pairs, 60 (0.6% of the total) revealed a verified fusion or fission event in either lineage after the divergence of O. sativa and A. thaliana. Polarizing these events by outgroup comparison revealed differences in the rate of gene fission but not of gene fusion in the rice and Arabidopsis lineages. Gene fission occurred at a higher rate than gene fusion in the O. sativa lineage and was furthermore more common in rice than in Arabidopsis. Nucleotide insertion bias has promoted gene fission in the O. sativa lineage, consistent with its generally longer nucleotide sequences than A. thaliana in selectively neutral regions, and with the abundance of transposable elements in rice. The divergence time of monocots and dicots (140-200 Myr) indicates that gene fusion/fission events occur at an average rate of 1x10(-11) to 2x10(-11) events per gene per year, approximately 100-fold slower than the average per site nuclear nucleotide substitution rate in these lineages. Gene fusion and fission are thus rare and slow processes in higher plant genomes; they should be of utility to address deeper evolutionary relationships among plants--and the relationship of plants to other eukaryotic lineages--where sequence-based phylogenies provide equivocal or conflicting results.

Arabidopsis↗
PubMed2006

An analysis of mobile genetic elements in three Plasmodium species and their potential impact on the nucleotide composition of the P. falciparum genome.

BACKGROUND: The completed genome sequences of the malaria parasites P. falciparum, P. y. yoelii and P. vivax have revealed some unusual features. P. falciparum contains the most AT rich genome sequenced so far--over 90% in some regions. In comparison, P. y. yoelii is approximately 77% and P. vivax is approximately 55% AT rich. The evolutionary reasons for these findings are unknown. Mobile genetic elements have a considerable impact on genome evolution but a thorough investigation of these elements in Plasmodium has not been undertaken. We therefore performed a comprehensive genome analysis of these elements and their derivatives in the three Plasmodium species. RESULTS: Whole genome analysis was performed using bioinformatic methods. Forty potential protein encoding sequences with features of transposable elements were identified in P. vivax, eight in P. y. yoelii and only six in P. falciparum. Further investigation of the six open reading frames in P. falciparum revealed that only one is potentially an active mobile genetic element. Most of the open reading frames identified in all three species are hypothetical proteins. Some represent annotated host proteins such as the putative telomerase reverse transcriptase genes in P. y. yoelii and P. falciparum. One of the P. vivax open reading frames identified in this study demonstrates similarity to telomerase reverse transcriptase and we conclude it to be the orthologue of this gene. CONCLUSION: There is a divergence in the frequencies of mobile genetic elements in the three Plasmodium species investigated. Despite the limitations of whole genome analytical methods, it is tempting to speculate that mobile genetic elements might have been a driving force behind the compositional bias of the P. falciparum genome.

Amino Acid Sequence↗
PubMed1995

A model for the evolution of the genome: the effect of stochasticity on genetic loads.

In this paper a general model is given for the evolution of the genome incorporating stochastic factors. The model is applied to the substitutional genetic load problem. All of the major hard selection load formulae in the literature are extended and, where necessary, corrected (for stochasticity). Turning to rank selection, formulae for stochastic factors are also corrected and harmful mutations included. A simple formula for the selection coefficient as a function of the nonneutral substitution rate and the mutation profile is obtained. Further, it is noted that the formulae derived also apply (for different parameter values) to the mutation load, thus unifying the two loads under a single theory. A general formula for the mutation load under hard selection is given, extending previous results. Finally, the author derives a formula showing how many harmful mutations can be effectively eliminated by rank selection and discusses its relevance to the question of the possible buildup of harmful mutations in the human gene pool due to long-term exposure to low-level radiation.

Animals↗
PubMed2005

Multi-alignment of orthologous genome regions in five species provides new insights into the evolutionary make-up of mammalian genomes.

Evidence has shown that bacterial genomes have undergone random shuffling of genomic elements consisting of one to two genes. In order to delineate such genome-shuffling events in mammals, we constructed a high-resolution map of Sus scrofa chromosome 3 (SSC3) with a total of 116 genes/markers. Alignment of this pig map to orthologous regions in human, dog, mouse and rat led to the identification of 31 provisional conserved ancestral blocks (CABs) in these five species. Among them, only 3 CABs (<10%) had one gene, indicating that one-gene shuffling is not frequent in mammals. The sizes of CABs vary significantly within a species, but each may be relatively consistent in different species with a scale to species-genome evolution. The type and frequency of rearrangement events that takes place, either intra- or interchromosomal, depends on the evolutionary regions and species under comparison. Characterization of 36 tentative breakpoint regions flanking these 31 CABs indicated that they occupied approximately 43 Mb in length and featured genome deserts, gene duplications, and birth/death of species-specific genes in humans. Identification of CABs provides an alternative for further determination of the evolutionary make-up of mammalian genomes.

Animals↗
PubMed1998

Genome size and GC-percent in vertebrates as determined by flow cytometry: the triangular relationship.

Genome size and GC-percent were determined by means of a special method of DNA flow cytometry in 154 vertebrate species. For the total dataset, a highly significant positive correlation was found between both parameters. The overall distribution of points is not linear but triangular: a wide range of GC-percent values is observed at the lower end of genome size range, whereas with an increase in genome size the lower limit for GC-percent is elevated, gradually approaching the upper limit (about 46%). In teleost fishes, which occupy the lower part of genome size range, the negative relationship between both parameters was observed. Two positive linear relationships were found between mean genome size and GC-percent of the main vertebrate groups (one includes fishes, amphibians, and mammals, the other consists of reptiles and birds, which show the higher GC-percent for their genome sizes). Distribution of variance between taxonomic levels indicates that GC-percent is more evolutionarily conservative than genome size in anamniotes. Anuran amphibians show the greatest part of genome size variability at the lower taxonomic levels as compared to other vertebrates (with no additional variance already above the genus level). The data obtained with different methods are compared. It is shown that the proposed method can provide useful data for studies on genome evolution and biodiversity.

Animals↗
PubMed2006

P elements and MITE relatives in the whole genome sequence of Anopheles gambiae.

BACKGROUND: Miniature Inverted-repeat Terminal Elements (MITEs), which are particular class-II transposable elements (TEs), play an important role in genome evolution, because they have very high copy numbers and display recurrent bursts of transposition. The 5' and 3' subterminal regions of a given MITE family often show a high sequence similarity with the corresponding regions of an autonomous Class-II TE family. However, the sustained presence over a prolonged evolutionary time of MITEs and TE master copies able to promote their mobility has been rarely reported within the same genome, and this raises fascinating evolutionary questions. RESULTS: We report here the presence of P transposable elements with related MITE families in the Anopheles gambiae genome. Using a TE annotation pipeline we have identified and analyzed all the P sequences in the sequenced A. gambiae PEST strain genome. More than 0.49% of the genome consists of P elements and derivates. P elements can be divided into 9 different subfamilies, separated by more than 30% of nucleotide divergence. Seven of them present full length copies. Ten MITE families are associated with 6 out of the 9 Psubfamilies. Comparing their intra-element nucleotide diversities and their structures allows us to propose the putative dynamics of their emergence. In particular, one MITE family which has a hybrid structure, with ends each of which is related to a different P-subfamily, suggests a new mechanism for their emergence and their mobility. CONCLUSION: This work contributes to a greater understanding of the relationship between full-length class-II TEs and MITEs, in this case P elements and their derivatives in the genome of A. gambiae. Moreover, it provides the most comprehensive catalogue to date of P-like transposons in this genome and provides convincing yet indirect evidence that some of the subfamilies have been recently active.

Animals↗