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PubMed2004

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.

We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.

Animals↗
PubMed2001

Evolution of the genomic systems of prokaryotes and its momentous consequences.

The earliest self-reproducing cell on Earth, our common ancestor, was probably as small as present-day bacteria. It gave rise to a very large and durable clone whose descendants must have been the only living occupants of the oceans for about one thousand million years. They reached astronomical numbers of separate, disjunct cells, and synthesized many new genes. Their small volume could not accommodate ever larger genomes and useful new genes replaced resident, less successful sequences, thus increasing diversity and the number of strains with highly specialized, distinct, bioenergetic potentialities. Also, selective pressure favored strains able to participate successfully in division of labor and in the sharing of diverse abilities in mixed communities, counterbalancing the limited capacities of individual genomes. Lateral gene transfer mechanisms appeared and were progressively improved, furthering the development of diversity. The prokaryotes' constructive evolution resulted in the formation of a worldwide web of genetic information, and a global bacterial superbiosystem (superorganism). By contrast, eukaryotic evolution of organisms has been typically Darwinian. Diversification of eukaryotic organisms was, however, considerably enriched and accelerated by symbioses with prokaryotes. The more broadly diversified bioenergetic potential of prokaryotes considerably increased the diversity of eukaryotes. Without their participation, our biosphere would have remained much less diverse and less dynamic. Environmental homeostasis has been maintained all along by guided bacterial evolution.

Evolution, Molecular↗
PubMed2003

Eukaryotic domain evolution inferred from genome comparisons.

Comparative analyses of eukaryotic genomes are providing insights into the mode and tempo of domain family evolution. Gene duplication, the source of family expansion, far exceeds the rate of emergence of domains from non-coding sequence, and the rate of recruitment of domains into novel architectures. Domain families that appear to be restricted to certain lineages are likely to be the result of gene duplication, coupled with rapid sequence diversification. If such families are evidence of past adaptation, then their functions must relate to the underlying mechanism of selection: competition among organisms.

Animals↗
PubMed1999

Molecular mechanisms of coxsackievirus persistence in chronic inflammatory myopathy: viral RNA persists through formation of a double-stranded complex without associated genomic mutations or evolution.

Enterovirus infection and persistence have been implicated in the pathogenesis of certain chronic muscle diseases. In vitro studies suggest that persistent enteroviruses mutate, evolving into forms that are less lytic and display altered tropism, but it is less clear whether these mechanisms operate in vivo. In this study, persistent coxsackievirus RNA from the muscle of mice afflicted with chronic inflammatory myopathy (CIM) was characterized and compared with RNA from a virus that had established a persistent infection of G8 mouse myoblasts for 30 passages in vitro. Competitive strand-specific reverse transcription-PCR and susceptibility to RNase I treatment revealed that plus- and minus-strand viral RNAs were present at nearly equivalent levels in muscle and that they persisted in a double-stranded conformation. All regions of the viral genome persisted and were amplified as a series of seven overlapping fragments. Restriction endonuclease fingerprinting coupled with sequencing indicated that there was no evolution of the viral genome associated with its persistence in muscle. This contrasted with the productive persistent infection that was established in myoblast cultures, where plus-strand RNA predominated and persistent virus developed distinct mutations. In vitro persistence proceeded by a carrier culture mechanism and was completely dependent on production of infectious virus, since persistent viral RNA was not detected in cultures subjected to antibody-mediated curing. These experiments demonstrate that persistence of coxsackievirus RNA in muscle is not facilitated by distinct genetic changes in the virus that give rise to replication-defective forms but occurs primarily through production of stable double-stranded RNA that is produced as the acute viral infection resolves. The data suggest a mechanism for coxsackievirus persistence in myofibers and perhaps other nondividing cells whereby cells that survive infection could harbor persistent viral RNA for extended times without producing detectable levels of infectious virus.

Animals↗
PubMed2006

Forest-tree population genomics and adaptive evolution.

Forest trees have gained much attention in recent years as nonclassical model eukaryotes for population, evolutionary and ecological genomic studies. Because of low domestication, large open-pollinated native populations, and high levels of both genetic and phenotypic variation, they are ideal organisms to unveil the molecular basis of population adaptive divergence in nature. Population genomics, in its broad-sense definition, is an emerging discipline that combines genome-wide sampling with traditional population genetic approaches to understanding evolution. Here we briefly review traditional methods of studying adaptive genetic variation in forest trees, and describe a new, integrated population genomics approach. First, alleles (haplotypes) at candidate genes for adaptive traits and their effects on phenotypes need to be characterized via sequencing and association mapping. At this stage, functional genomics can assist in understanding gene action and regulation by providing detailed transcriptional profiles. Second, frequencies of alleles in native populations for causative single-nucleotide polymorphisms are estimated to identify patterns of adaptive variation across heterogeneous environments. Population genomics, through deciphering allelic effects on phenotypes and identifying patterns of adaptive variation at the landscape level, will in the future constitute a useful tool, if cost-effective, to design conservation strategies for forest trees.

Adaptation, Physiological↗
PubMed1993

A model simulating the dynamics of plant mitochondrial genomes.

Molecular evolution of the plant mitochondrial genome involves rearrangements due to the presence of highly recombining repeated sequences. As a result, this genome is composed of a set of molecules of various sizes that generate each other through recombination. The model presented simulates the evolution of various frequencies of the different types of molecules over successive cell cycles. It considers the mitochondrial genome as a population of circular molecules evolving through recombination, replication and random segregation. The model parameters are the rates of recombination of each sequence, the frequency of each type of recombination, the replication rates of the circles and the total amount of mitochondrial DNA per cell. This model demonstrates that high recombination rates lead to rapid deletions of sequences in the absence of selection. The frequency of deletion is dependent on the simulated reproductive mechanism. The conditions leading to reversible or irreversible rearrangements were also investigated.

Biological Evolution↗
PubMed2001

Deletional bias and the evolution of bacterial genomes.

Although bacteria increase their DNA content through horizontal transfer and gene duplication, their genomes remain small and, in particular, lack nonfunctional sequences. This pattern is most readily explained by a pervasive bias towards higher numbers of deletions than insertions. When selection is not strong enough to maintain them, genes are lost in large deletions or inactivated and subsequently eroded. Gene inactivation and loss are particularly apparent in obligate parasites and symbionts, in which dramatic reductions in genome size can result not from selection to lose DNA, but from decreased selection to maintain gene functionality. Here we discuss the evidence showing that deletional bias is a major force that shapes bacterial genomes.

Bacteria↗
PubMed2006

Gene order data from a model amphibian (Ambystoma): new perspectives on vertebrate genome structure and evolution.

BACKGROUND: Because amphibians arise from a branch of the vertebrate evolutionary tree that is juxtaposed between fishes and amniotes, they provide important comparative perspective for reconstructing character changes that have occurred during vertebrate evolution. Here, we report the first comparative study of vertebrate genome structure that includes a representative amphibian. We used 491 transcribed sequences from a salamander (Ambystoma) genetic map and whole genome assemblies for human, mouse, rat, dog, chicken, zebrafish, and the freshwater pufferfish Tetraodon nigroviridis to compare gene orders and rearrangement rates. RESULTS: Ambystoma has experienced a rate of genome rearrangement that is substantially lower than mammalian species but similar to that of chicken and fish. Overall, we found greater conservation of genome structure between Ambystoma and tetrapod vertebrates, nevertheless, 57% of Ambystoma-fish orthologs are found in conserved syntenies of four or more genes. Comparisons between Ambystoma and amniotes reveal extensive conservation of segmental homology for 57% of the presumptive Ambystoma-amniote orthologs. CONCLUSION: Our analyses suggest relatively constant interchromosomal rearrangement rates from the euteleost ancestor to the origin of mammals and illustrate the utility of amphibian mapping data in establishing ancestral amniote and tetrapod gene orders. Comparisons between Ambystoma and amniotes reveal some of the key events that have structured the human genome since diversification of the ancestral amniote lineage.

Ambystoma↗
PubMed1996

Genome research and evolution in trypanosomes.

Trypanosoma brucei and Trypanosoma cruzi cause different human diseases. As strategies for immune evasion, T. brucei undergone antigenic variation whereas T. cruzi becomes an intracellular organism. This fundamental difference is reflected by major differences in their genome organizations. Recent comparisons of their gene sequences indicate that these two trypanosome species are highly divergent evolutionarily.

Animals↗
PubMed1983

Human mitochondrial genome and the evolution of methionine transfer ribonucleic acids.

The recently deciphered sequence of the human mitochondrial genome is analyzed in the light of an archigenetic hypothesis, according to which mitochondria are derived neither from pro- nor eukaryotes but from more primitive organisms. The possibility that animal mitochondria have only one gene both for elongator and initiator methionine tRNA is supported but C-A pair forming cytosine in the anticodon of these tRNAs is considered to be unmodified. The evolution of the gene and of the codon reading pattern of methionine tRNA is discussed.

Animals↗
PubMed2002

Genome dynamics and evolution of the Mla (powdery mildew) resistance locus in barley.

Genes that confer defense against pathogens often are clustered in the genome and evolve via diverse mechanisms. To evaluate the organization and content of a major defense gene complex in cereals, we determined the complete sequence of a 261-kb BAC contig from barley cv Morex that spans the Mla (powdery mildew) resistance locus. Among the 32 predicted genes on this contig, 15 are associated with plant defense responses; 6 of these are associated with defense responses to powdery mildew disease but function in different signaling pathways. The Mla region is organized as three gene-rich islands separated by two nested complexes of transposable elements and a 45-kb gene-poor region. A heterochromatic-like region is positioned directly proximal to Mla and is composed of a gene-poor core with 17 families of diverse tandem repeats that overlap a hypermethylated, but transcriptionally active, gene-dense island. Paleontology analysis of long terminal repeat retrotransposons indicates that the present Mla region evolved over a period of >7 million years through a variety of duplication, inversion, and transposon-insertion events. Sequence-based recombination estimates indicate that R genes positioned adjacent to nested long terminal repeat retrotransposons, such as Mla, do not favor recombination as a means of diversification. We present a model for the evolution of the Mla region that encompasses several emerging features of large cereal genomes.

DNA Methylation↗
PubMed2026

Genome-wide cyclin gene evolution in Arabidopsis and Brassica reveals polyploidization-driven duplication and flowering-time associations.

Cyclin genes are plant cell cycle regulators that play essential roles in growth, development, and reproduction. However, the evolutionary dynamics and genomic organization of cyclin genes across the Brassicaceae family remain poorly understood, particularly in the context of allotetraploid genome evolution. Here, we investigated the diversity, expansion mechanisms, and potential functional diversification of cyclin genes across ten Brassicaceae genomes, including four Arabidopsis and six Brassica species. A total of 1087 cyclin genes representing 23 cyclin types were identified. Comparative genomic analyses revealed that cyclin gene expansion was strongly influenced by polyploidization in Brassica species, with 1845 duplication events involving 1063 genes. Whole-genome duplication was the predominant mechanism driving expansion, while both inter- and intra-genomic duplications contributed to gene retention in tetraploid Brassica species, with the highest duplication frequency observed in Brassica juncea. Across genomes, 120 physical gene clusters were identified, including homogeneous and heterogeneous types. Ortholog analysis between progenitor and allotetraploid species identified 852 orthologous pairs involving 366 genes, indicating extensive conservation following allotetraploid formation. Phylogenetic analysis resolved cyclins into three major clades, while expression-based clustering in Brassica napus grouped genes into four major clusters, suggesting functional diversification. Integration of pan-genomic and flowering-time QTL analyses further identified two cyclin genes, Bna21cycA2 and Bna113cycD4, which contain amino acid polymorphisms and represent putative candidate variations potentially associated with flowering-time variation across multiple genomes. These findings provide new insights into the evolutionary expansion, retention, and potential functional divergence of cyclin genes in Brassicaceae and highlight candidate loci for future functional studies and crop improvement.

Evolution, Molecular↗
PubMed2005

Fold usage on genomes and protein fold evolution.

We review fold usage on completed genomes to explore protein structure evolution. The patterns of presence or absence of folds on genomes gives us insights into the relationships between folds, the age of different folds and how we have arrived at the set of folds we see today. We examine the relationships between different measures which describe protein fold usage, such as the number of copies of a fold per genome, the number of families per fold, and the number of genomes a fold occurs on. We obtained these measures of fold usage by searching for the structural domains on 157 completed genome sequences from all three kingdoms of life. In our comparisons of these measures we found that bacteria have relatively more distinct folds on their genomes than archaea. Eukaryotes were found to have many more copies of a fold on their genomes. If we separate out the different fold classes, the alpha/beta class has relatively fewer distinct folds on large genomes, more copies of a fold on bacteria and more folds occurring in all three kingdoms simultaneously. These results possibly indicate that most alpha/beta folds originated earlier than other folds. The expected power law distribution is observed for copies of a fold per genome and we found a similar distribution for the number of families per fold. However, a more complicated distribution appears for fold occurrence across genomes, which strongly depends on fold class and kingdom. We also show that there is not a clear relationship between the three measures of fold usage. A fold which occurs on many genomes does not necessarily have many copies on each genome. Similarly, folds with many copies do not necessarily have many families or vice versa.

Archaeal Proteins↗
PubMed2006

Retrogene movement within- and between-chromosomes in the evolution of Drosophila genomes.

Recent genomic analyses in Drosophila and mammals of inter-chromosomal retroposition have revealed that during evolution the retroposed genes that show male-biased expression tend to leave the X chromosome and opt for autosomal positions. Such a phenomenon may be a process of general, genomic and evolutionary relevance. It contributed to the unexpected overrepresentation of male-biased genes on the autosomes recently observed in microarray expression experiments. In this paper, we report our genomic analysis of within-chromosomal retroposition in Drosophila melanogaster, and compare it with the previously identified pattern of the between-chromosomal retroposition. We find that a surfeit of autosomal retroposed genes originated from parental genes located on the same chromosome, in contrast to the X chromosome in which only few genes retroposed in cis. Such an autosomal proximity effect implicates a role of the mutation process for retroposition in determining chromosomal locations of autosome-derived retroposed genes. Furthermore, this phenomenon supports the hypothesis that natural selection favors the retroposition of genes out of the X chromosome. Analyses of a large expression database for D. melanogaster genes revealed that the vast majority of the X-derived autosomal retroposed genes had evolved testis expression functions, consistent with other previous genomic analyses.

Animals↗
PubMedDate not supplied

The application of molecular phylogenetics to the analysis of viral genome diversity and evolution.

DNA sequencing and molecular phylogenetics are increasingly being used in virology laboratories to study the transmission of viruses. By reconstructing the evolutionary history of viral genomes the behaviour of viral populations can be modelled, and the future of epidemics may be forecast. The manner in which such viral DNA sequences are analysed is the focus of this review. Many researchers resort to the often-quoted 'black box' approach because phylogenetics theory can be daunting, and phylogenetics software packages can appear to be difficult to use. However, because phylogenetic analyses are often used in important and sensitive arenas, for example to provide evidence indicating transmission between persons, it is vital that appropriate care is taken to estimate reliably true relationships. In this review, we discuss how a molecular phylogenetics study should be approached, give an overview of the methods and programs for analysing DNA sequence data, and point readers to appropriate texts for further details. The aim of this review, therefore, is to provide researchers with an easy to understand guide to molecular phylogenetics, with special reference to viral genomes.

Amino Acid Sequence↗