The evolution of the adenoviral genome.
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Adenoviridae↗
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Results for “Genome evolution”
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Genomic potential hypothesis of evolution: a concept of biogenesis in habitable spaces of the universe.
The new hypothesis of evolution establishes a contiguity of life sciences with cosmology, physics, and chemistry, and provides a basis for the search for life on other planets. Chemistry is the sole driving force of the assembly of life, under the subtle guidance exerted by bonding orbital geometry. That phenomenon leads to multiple origins that function on the same principles but are different to the extent that their nucleic acid core varies. Thus, thoughts about the origins of life and the development of complexity have been transferred from the chance orientation of the past to the realm of atomic structures, which are subject to the laws of thermodynamics and kinetics. Evolution is a legitimate subject of basic science, and the complexity of life will submit to the laws of chemistry and physics as the problem is viewed from a new perspective. The paradigm connects life to the big events that formed every sphere of our living space and that keeps conditions fine-tuned for life to persist, perhaps a billion years or more. The "genomic potential" hypothesis leads to the prediction that life like ours is likely to exist in galaxies that are as distant from the origin of the universe as the Milky Way, and that the habitable zone of our galaxy harbors other living planets as well.
Biological Evolution↗
Isolation and characterization of rat and human glyceraldehyde-3-phosphate dehydrogenase cDNAs: genomic complexity and molecular evolution of the gene.
Full length cDNAs encoding the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from rat and man have been isolated and sequenced. Many GAPDH gene-related sequences have been found in both genomes based on genomic blot hybridization analysis. Only one functional gene product is known. Results from genomic library screenings suggest that there are 300-400 copies of these sequences in the rat genome and approximately 100 in the human genome. Some of these related sequences have been shown to be processed pseudogenes. We have isolated several rat cDNA clones corresponding to these pseudogenes indicating that some pseudogenes are transcribed. Rat and human cDNAs are 89% homologous in the coding region, and 76% homologous in the first 100 base pairs of the 3'-noncoding region. Comparison of these two cDNA sequences with those of the chicken, Drosophila and yeast genes allows the analysis of the evolution of the GAPDH genes in detail.
Amino Acid Sequence↗
Monoclonality and surface lesion-specific microsatellite alterations in premalignant and malignant neoplasia of uterine cervix: a local field effect of genomic instability and clonal evolution.
Invasive squamous carcinoma of the uterine cervix (CC) arises from sequential progression of low-grade (L) and high-grade (H) squamous intraepithelial lesions (SILs). In clinical observations, these lesions are frequently found as synchronous multiple foci. The nature and evolutionary mechanism of these lesions are largely unknown. We have performed allelotyping of three 3p markers (at 3p14, 3p22-24, and 3p25) on 22 LSILs and 15 HSILs microdissected from patients with multiple (n = 21) or uniform (n = 6) cervical lesions. The results were analyzed together with our previous allelotyping of 57 deeply invasive CCs. Loss of heterozygosity at one of the three markers was observed in 23%, 27%, and 31 % of LSILs, HSILs, and CCs, respectively. Frequent and early allelic loss was noted (in 30% of LSILs and 50% of HSILs) at 3p14, which may harbor tumor suppressor genes involved in early stages of cervical carcinogenesis. A high frequency of microsatellite alteration (MA) was found in LSIL (41%) and HSIL (67%) but not in CC (5.3%). In particular, MA was more frequently found in low-grade lesions in association with invasive cancers (75%, 6/8) than in those associated with SILs (29%, 4/14) (P < 0.05). Together with the finding of a monoclonal origin of premalignant and malignant cervical lesions, the present results allow us to propose a model of local field effect of genomic instability that progressively affects the clonal evolution of SIL of uterine cervix.
Carcinoma in Situ↗
Retroviruses and evolution.
A wide variety of different genetic elements and DNA sequences have used reverse transcription in their replication or transposition. Some of these elements may be evolutionarily related and show a continued evolution to autonomy from the cell genome. The evolution of a cancer reflects a similar drive for autonomy from the organism.
Biological Evolution↗
The spinal muscular atrophy gene region at 5q13.1 has a paralogous chromosomal region at 6p21.3.
Paralogous regions are duplicated segments of chromosomal DNA that have been acquired during the evolution of the genome. Subsequent divergent evolution of the genes within paralogous regions can lead to the formation of gene families. Here, we report the identification of a region on Chromosome (Chr) 6 at 6p21.3 that is paralogous with the Spinal Muscular Atrophy (SMA) gene region on Chr 5 at 5q13.1. Partial characterization of this region identified nine sequences all of which are highly homologous to DNA sequences of the SMA gene region at 5q13.1. These sequences include four beta-glucuronidase sequences, two retrotransposon sequences, a novel cDNA, a Sequence Tagged Site (STS), and one that is homologous to exon 9 of the Neuronal Apoptosis Inhibitor Protein (NAIP) gene. The 6p21.3 paralogous SMA region may contain genes that are related to those in the SMA region at 5q13.1; however, a direct association of this region with SMA is unlikely given that no linkage of SMA with Chr 6 has been reported.
Base Sequence↗
Entering the total-genomic era.
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Evolution, Molecular↗
Evolution of organelles and eukaryotic genomes.
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Animals↗
Genomic islands and the evolution of catabolic pathways in bacteria.
Genes for the degradation of organic pollutants have usually been allocated to plasmid DNAs in bacteria or considered non-mobile when detected in the chromosome. New discoveries have shown that catabolic genes can also be part of so-called integrative and conjugative elements (ICElands), a group of mobile DNA elements also known as genomic islands and conjugative transposons. One such ICEland is the clc element for chlorobenzoate and chlorocatechol degradation in Pseudomonas sp. strain B13. Genome comparisons and genetic data on integrase functioning reveal that the clc element and several other unclassified ICElands belong to a group of elements with conserved features. The clc element is unique among them in carrying the genetic information for several degradation pathways, whereas the others give evidence for pathogenicity functions. Many more such elements may exist, bridging the gap between pathogenicity and degradation functions.
Catalysis↗
The compositional evolution of the murid genome.
Murid rodents show much less variation in isochore base composition than do most other mammals, a difference which has been referred to as the murid shift. We have investigated the murid shift by asking (1) whether the murid shift is ongoing and (2) whether there is any evidence of selection or biased gene conversion affecting base composition in the present-day mouse genome. By estimating the ancestral base composition of protein-coding genes in murids we can confirm that the murid shift is ongoing. Tests using nongenic polymorphism data fail to reject the hypothesis that base composition is due to mutation bias alone. However, the patterns of compositional change suggested by the polymorphism and divergence data differ, suggesting the possibility of two murid shifts.
Animals↗
Large-scale Genome Analyses Provide Insights into Hymenoptera Evolution.
The order Hymenoptera includes a large number of species with diverse lifestyles and is known for its significant contributions to natural ecosystems. To better understand the evolution of this diverse order, we performed large-scale comparative genomics on 131 species from 13 superfamilies, covering most representative groups. We used these genomes to reveal an overall pattern of genomic change in terms of gene content and evolutionary rate throughout hymenopteran history. We identified genes that possibly contributed to the evolution of several key innovations, such as parasitoidism, wasp-waist, stinger, and secondary phytophagy. We also discovered the distinct genomic trajectories between the clade containing major parasitoid wasps (Parasitoida) and stinging species (Aculeata) since their divergence, which are involved in many aspects of genomic change, such as rapidly evolving gene families, gene gain and loss, and metabolic pathway evolution. In addition, we explored the genomic features accompanying the three independent evolution of secondary phytophagy. Our work provides insights for understanding genome evolution and the genomic basis of diversification in Hymenoptera.
Animals↗
Genomics. Gene duplication and evolution.
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Animals↗
Genomic structure, chromosomal location, and evolution of the mouse Hox 8 gene.
We isolated genomic clones containing the mouse Hox 8 gene, a member of the msh gene family. We show that Hox 8 comprises two exons of approximately 600 and 691 bp separated by a 3.5-kb intron, and that it cosegregates with previously mapped markers in the distal region of mouse chromosome 13. In midgestation embryos, the Hox 8 gene produces transcripts of 1.4 and 2.2 kb. Both transcripts are present in facial tissues of the newborn mouse, though the ratio of the 2.2-kb transcript to the 1.4-kb transcript is reduced relative to the ratio observed for midgestation embryos. An alignment of the homeobox sequences of previously characterized members of the msh family revealed three subclasses: Hox 7-like genes, Hox 8-like genes, and msh-like genes. Both the Hox 7-like genes and Hox 8-like genes are present throughout the vertebrates. Representatives of the third subclass, the msh-like genes, are found in a protostome (Drosophila) and a deuterostome (Ciona) and are thus likely to be phylogenetically widespread. To investigate the distribution of Hox 8-like genes outside the chordates, we used the polymerase chain reaction and degenerate Hox 8 primers to screen genomic DNA of the purple sea urchin (Strongylocentrotus purpuratus, Phylum Echinodermata). We isolated a gene with greater sequence similarity to mouse Hox 8 than to members of the Hox 7 or msh subfamilies, demonstrating that the Hox 8 subfamily has been in existence at least since the echinoderms diverged from the lineage that gave rise to the chordates.(ABSTRACT TRUNCATED AT 250 WORDS)
Amino Acid Sequence↗
Microsatellite evolution in the mitochondrial genome of Bechstein's bat (Myotis bechsteinii).
Being highly polymorphic, microsatellites are widely used genetic markers. They are abundant throughout the nuclear genomes of eukaryotes but rare in the mitochondrial genomes (mtDNA) of animals. We describe a short but highly polymorphic AT microsatellite in the mtDNA control region of Bechstein's bat and discuss the role of mutation, genetic drift, and selection in maintaining its variability. As heteroplasmy and hence mutation rate were positively correlated with repeat number, a simple mutation model cannot explain the observed frequency distribution of AT copy numbers. Because of the unimodal distribution of repeat numbers found in heteroplasmic individuals, single step mutations are likely to be the predominant mechanism of copy number alternations. Above a certain copy number (seven repeats), deletions of single dinucleotide repeats seem to be more common than additions, which results in a decrease in frequency of long alleles. Heteroplasmy was inherited from mothers to their offspring and no evidence of paternal inheritance of mitochondria was found. Genetic differences accumulated with more distant ancestry, which suggests that microsatellites can be useful genetic markers in population genetics.
Animals↗
Phylogenetic analyses alone are insufficient to determine whether genome duplication(s) occurred during early vertebrate evolution.
The widely accepted notion that two whole-genome duplications occurred during early vertebrate evolution (the 2R hypothesis) stems from the fact that vertebrates often possess several genes corresponding to a single invertebrate homolog. However the number of genes predicted by the Human Genome Project is less than twice as many as in the Drosophila melanogaster or Caenorhabditis elegans genomes. This ratio could be explained by two rounds of genome duplication followed by extensive gene loss, by a single genome duplication, by sequential local duplications, or by a combination of any of the above. The traditional method used to distinguish between these possibilities is to reconstruct the phylogenetic relationships of vertebrate genes to their invertebrate orthologs; ratios of invertebrate-to-vertebrate counterparts are then used to infer the number of gene duplication events. The lancelet, amphioxus, is the closest living invertebrate relative of the vertebrates, and unlike protostomes such as flies or nematodes, is therefore the most appropriate outgroup for understanding the genomic composition of the last common ancestor of all vertebrates. We analyzed the relationships of all available amphioxus genes to their vertebrate homologs. In most cases, one to three vertebrate genes are orthologous to each amphioxus gene (median number=2). Clearly this result, and those of previous studies using this approach, cannot distinguish between alternative scenarios of chordate genome expansion. We conclude that phylogenetic analyses alone will never be sufficient to determine whether genome duplication(s) occurred during early chordate evolution, and argue that a "phylogenomic" approach, which compares paralogous clusters of linked genes from complete amphioxus and human genome sequences, will be required if the pattern and process of early chordate genome evolution is ever to be reconstructed.
Animals↗
A novel gene family NBPF: intricate structure generated by gene duplications during primate evolution.
Partial and complete genome duplications occurred during evolution and resulted in the creation of new genes and gene families. We identified a novel and intricate human gene family located primarily in regions of segmental duplications on human chromosome 1. We named it NBPF, for neuroblastoma breakpoint family, because one of its members is disrupted by a chromosomal translocation in a neuroblastoma patient. The NBPF genes have a repetitive structure with high intragenic and intergenic sequence similarity in both coding and noncoding regions. These similarities might expose these genomic regions to illegitimate recombination, resulting in structural variation in the NBPF genes. The encoded proteins contain a highly conserved domain of unknown function, which we have named the NBPF repeat. In silico analysis combined with the isolation of multiple full-length cDNA clones showed that several members of this gene family are abundantly expressed in a large variety of tissues and cell lines. Strikingly, no discernable orthologues could be identified in the completed genomes of fruit fly, nematode, mouse, or rat, but sequences with low homology could be isolated from the draft canine and bovine genomes. Interestingly, this gene family shows primate-specific duplications that result in species-specific arrays of NBPF homologous sequences. Overall, this novel NBPF family reflects the continuous evolution of primate genomes that resulted in large physiological differences, and its potential role in this process is discussed.
Amino Acid Sequence↗
Analysis of vertebrate genomes suggests a new model for clade B serpin evolution.
BACKGROUND: The human genome contains 13 clade B serpin genes at two loci, 6p25 and 18q21. The three genes at 6p25 all conform to a 7-exon gene structure with conserved intron positioning and phasing, however, at 18q21 there are two 7-exon genes and eight genes with an additional exon yielding an 8-exon structure. Currently, it is not known how these two loci evolved, nor which gene structure arose first--did the 8-exon genes gain an exon, or did the 7-exon genes lose one? Here we use the genomes of diverse vertebrate species to plot the emergence of clade B serpin genes and to identify the point at which the two genomic structures arose. RESULTS: Analysis of the chicken genome indicated the presence of a single clade B serpin gene locus, containing orthologues of both human loci and both genomic structures. The frog genome and the genomes of three fish species presented progressively simpler loci, although only the 7-exon structure could be identified. The Serpinb12 gene contains seven exons in the frog genome, but eight exons in chickens and humans, indicating that the additional exon evolved in this gene. CONCLUSION: We propose a new model for clade B serpin evolution from a single 7-exon gene (either Serpinb1 or Serpinb6). An additional exon was gained in the Serpinb12 gene between the tetrapoda and amniota radiations to produce the 8-exon structure. Both structures were then duplicated at a single locus until a chromosomal breakage occurred at some point along the mammalian lineage resulting in the two modern loci.
Animals↗