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Results for “Genome evolution”

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At least 1,117 records · Page 62Linked to original sources
PubMed1999

Evolution of organellar genomes.

Accumulating molecular data, particularly complete organellar genome sequences, continue to advance our understanding of the evolution of mitochondrial and chloroplast DNAs. Although the notion of a single primary origin for each organelle has been reinforced, new models have been proposed that tie the acquisition of mitochondria more closely to the origin of the eukaryotic cell per se than is implied by classic endosymbiont theory. The form and content of the ancestral proto-mitochondrial and proto-chloroplast genomes are becoming clearer but unusual patterns of organellar genome structure and organization continue to be discovered. The 'single-gene circle' arrangement recently reported for dinoflagellate chloroplast genomes is a notable example of a highly derived organellar genome.

Animals↗
PubMed1998

Characterization of a novel class of interspersed LTR elements in primate genomes: structure, genomic distribution, and evolution.

Retrovirus-like sequences and their solitary (solo) long terminal repeats (LTRs) are common repetitive elements in eukaryotic genomes. We reported previously that the tandemly arrayed genes encoding U2 snRNA (the RNU2 locus) in humans and apes contain a solo LTR (U2-LTR) which was presumably generated by homologous recombination between the two LTRs of an ancestral provirus that is retained in the orthologous baboon RNU2 locus. We have now sequenced the orthologous U2-LTRs in human, chimpanzee, gorilla, orangutan, and baboon and examined numerous homologs of the U2-LTR that are dispersed throughout the human genome. Although these U2-LTR homologs have been collectively referred to as LTR13 in the literature, they do not display sequence similarity to any known retroviral LTRs; however, the structure of LTR13 closely resembles that of other retroviral LTRs with a putative promoter, polyadenylation signal, and a tandemly repeated 53-bp enhancer-like element. Genomic blotting indicates that LTR13 is primate-specific; based on sequence analysis, we estimate there are about 2,500 LTR13 elements in the human genome. Comparison of the primate U2-LTR sequences suggests that the homologous recombination event that gave rise to the solo U2-LTR occurred soon after insertion of the ancestral provirus into the ancestral U2 tandem array. Phylogenetic analysis of the LTR13 family confirms that it is diverse, but the orthologous U2-LTRs form a coherent group in which chimpanzee is closest to the humans; orangutan is a clear outgroup of human, chimpanzee, and gorilla; and baboon is a distant relative of human, chimpanzee, gorilla, and orangutan. We compare the LTR13 family with other known LTRs and consider whether these LTRs might play a role in concerted evolution of the primate RNU2 locus.

Animals↗
PubMedDate not supplied

[Concept of a bacterial species and the evolution of the prokaryotic genome].

The present concepts of evolution and species delineation in prokaryotes are considered. Recently a considerable extension of knowledge on the processes of microevolution of medically significant bacteria was noted alongside with the importance of horizontal and lateral transfer of genes. The phylophenetic concept of species was considered in detail. The inclusion of the ecological criterion into a phylophenetic concept of a species is supposed to facilitate the development of more adequate notion on the evolution of bacteria, the improvement of species delineation in prokaryotes, their classification and nomenclature.

Bacteria↗
PubMed2007

Recombination: an underappreciated factor in the evolution of plant genomes.

Our knowledge of recombination rates and patterns in plants is far from being comprehensive. However, compelling evidence indicates a central role for recombination, through its influences on mutation and selection, in the evolution of plant genomes. Furthermore, recombination seems to be generally higher and more variable in plants than in animals, which could be one of the primary reasons for differences in genome lability between these two kingdoms. Much additional study of recombination in plants is needed to investigate these ideas further.

Animals↗
PubMed2006

Genomic organization and evolution of the 5S ribosomal DNA in Tilapiini fishes.

5S rDNA sequences present an intense dynamism and have proved to be valuable as genetic markers to distinguish closed related species and also in the understanding of the evolutionary dynamic of repetitive sequences in the genomes. In order to identify patterns of 5S rDNA organization and their evolution in the genome of fish species, such genomic segment was investigated in the tilapias Oreochromis niloticus and Tilapia rendalli, and in the hybrid O. urolepis hornorum x O. mossambicus. A dual 5S rDNA system was identified in the three analyzed tilapia samples. Although each 5S rDNA class was conserved among the three samples, a distinct 5S rDNA genome organization pattern could be evidenced for each sample. The presence of a dual 5S rDNA system seems to be a general trait among non-related teleost fish orders, suggesting that evolutionary events of duplication have occurred before the divergence of the main groups of teleost fishes.

Animals↗
PubMed1986

Why mitochondria need a genome.

The evolution of the mitochondrial genome towards the compact organization found in the higher eukaryotes is discussed. It is suggested that the machinery for co-translational protein export across the endoplasmic reticulum membrane sets strict limits on the kinds of protein-coding genes that can be successfully transferred from the mitochondrial to the nuclear genome. This hypothesis is in perfect agreement with the pattern of mitochondrially vs nuclearly encoded mitochondrial proteins found in species such as man, mouse, and Xenopus.

Amino Acid Sequence↗
PubMed1997

Correlated rates of synonymous site evolution across plant genomes.

Synonymous substitution rates have been shown to vary among evolutionary lineages of both nuclear and organellar genes across a broad range of taxonomic groups. In animals, rate heterogeneity does not appear to be correlated across nuclear and mitochondrial genes. In this paper, we contrast substitution rates in two plant groups and show that grasses evolve more rapidly than palms at synonymous sites in a mitochondrial, a nuclear, and a plastid gene. Furthermore, we show that the relative rates of synonymous substitution between grasses and palms are similar at the three loci. The correlation in synonymous substitution rates across genes is particularly striking because the three genes evolve at very different absolute rates. In contrast, relative rates of nonsynonymous substitution are not conserved among the three genes.

Alcohol Dehydrogenase↗
PubMed2002

Genomic sequence and evolution of marine cyanophage P60: a new insight on lytic and lysogenic phages.

The genome of cyanophage P60, a lytic virus which infects marine Synechococcus WH7803, was completely sequenced. The P60 genome contained 47,872 bp with 80 potential open reading frames that were mostly similar to the genes found in lytic phages like T7, phi-YeO3-12, and SIO1. The DNA replication system, consisting of primase-helicase and DNA polymerase, appeared to be more conserved in podoviruses than in siphoviruses and myoviruses, suggesting that DNA replication genes could be the critical elements for lytic phages. Strikingly high sequence similarities in the regions coding for nucleotide metabolism were found between cyanophage P60 and marine unicellular cyanobacteria.

Bacteriophages↗
PubMed2004

Further statistical analysis for genome-wide expression evolution in primate brain/liver/fibroblast tissues.

In spite of only a 1-2 per cent genomic DNA sequence difference, humans and chimpanzees differ considerably in behaviour and cognition. Affymetrix microarray technology provides a novel approach to addressing a long-term debate on whether the difference between humans and chimpanzees results from the alteration of gene expressions. Here, we used several statistical methods (distance method, two-sample t-tests, regularised t-tests, ANOVA and bootstrapping) to detect the differential expression pattern between humans and great apes. Our analysis shows that the pattern we observed before is robust against various statistical methods; that is, the pronounced expression changes occurred on the human lineage after the split from chimpanzees, and that the dramatic brain expression alterations in humans may be mainly driven by a set of genes with increased expression (up-regulated) rather than decreased expression (down-regulated).

Animals↗
PubMed1991

RNA viruses: genome structure and evolution.

The explosive pace of sequencing of RNA viruses is leading to rapid advances in our understanding of the evolution of these viruses and of the ways in which their genomes are organized and expressed. New insights are coming not only from genomic nucleotide sequence comparisons, but also from direct sequencing of transcribed mRNAs and of RNAs that serve as intermediates in replication.

Biological Evolution↗
PubMed2026

Comparative Analysis of Chloroplast Genomes Reveals Molecular Evolution and Phylogenetic Relationships in Fraxinus (Fraxinus mandshurica).

Fraxinus mandshurica (Manchurian ash) is an ecologically and economically valuable hardwood tree native to Northeast Asia, yet its genomic resources remain limited. We assembled its complete chloroplast (cp) genome (155,559 bp) using hybrid PacBio and Illumina sequencing and performed comparative, phylogenetic, and evolutionary analyses. The cp genome exhibits a typical quadripartite structure encoding 132 gene copies, comprising 114 unique genes (80 protein-coding, 30 tRNA, and 4 rRNA genes), with 18 genes duplicated in the inverted repeat (IR) regions. Simple sequence repeat analysis revealed dominance of mononucleotide A/T repeats. Phylogenetic analysis of 53 complete cp genomes strongly supported the monophyly of Oleaceae and resolved F. mandshurica as sister to the North American F. nigra, consistent with previously proposed Miocene intercontinental dispersal scenarios between East Asia and North America. Most protein-coding genes were under strong purifying selection (Ka/Ks << 1), whereas petB, rpl2, and several ndh genes showed elevated Ka/Ks values that are suggestive of altered selective constraint but are based on very few substitutions and are therefore not, on their own, evidence of positive selection. Nucleotide diversity (Pi) analysis identified 15 hypervariable intergenic spacers (mean Pi = 0.067), among which trnM-CAU-rps14, ndhJ-ndhK, and petL-petG represent promising candidate barcode regions requiring further validation. This study provides a high-quality, fully annotated cp genome of F. mandshurica and a valuable genomic resource for future phylogenetic, population genetic, and conservation studies of this important genus.

Fraxinus↗
PubMed1993

SecA is plastid-encoded in a red alga: implications for the evolution of plastid genomes and the thylakoid protein import apparatus.

Partial sequence analysis of the plastid DNA (ptDNA) from a red alga, Antithamnion sp., revealed the presence of a homologue to the Escherichia coli secA gene as well as two open reading frames (ORF 510, ORF 179). In addition a sec Y homologue has been detected on the plastid genome by heterologous hybridization. None of these genes has been found in completely sequenced chlorophytic plastid genomes. SecA and secY gene copies were also detected in the ptDNA of a chromophytic alga, indicating that secA Y may be ubiquitous in rhodophytes and chromophytes. The significance of these findings for the evolution of plastid genomes and the thylakoid protein import mechanism is discussed.

Adenosine Triphosphatases↗
PubMed2006

Chromosome organization and chromatin modification: influence on genome function and evolution.

Histone modifications of nucleosomes distinguish euchromatic from heterochromatic chromatin states, distinguish gene regulation in eukaryotes from that of prokaryotes, and appear to allow eukaryotes to focus recombination events on regions of highest gene concentrations. Four additional epigenetic mechanisms that regulate commitment of cell lineages to their differentiated states are involved in the inheritance of differentiated states, e.g., DNA methylation, RNA interference, gene repositioning between interphase compartments, and gene replication time. The number of additional mechanisms used increases with the taxon's somatic complexity. The ability of siRNA transcribed from one locus to target, in trans, RNAi-associated nucleation of heterochromatin in distal, but complementary, loci seems central to orchestration of chromatin states along chromosomes. Most genes are inactive when heterochromatic. However, genes within beta-heterochromatin actually require the heterochromatic state for their activity, a property that uniquely positions such genes as sources of siRNA to target heterochromatinization of both the source locus and distal loci. Vertebrate chromosomes are organized into permanent structures that, during S-phase, regulate simultaneous firing of replicon clusters. The late replicating clusters, seen as G-bands during metaphase and as meiotic chromomeres during meiosis, epitomize an ontological utilization of all five self-reinforcing epigenetic mechanisms to regulate the reversible chromatin state called facultative (conditional) heterochromatin. Alternating euchromatin/heterochromatin domains separated by band boundaries, and interphase repositioning of G-band genes during ontological commitment can impose constraints on both meiotic interactions and mammalian karyotype evolution.

Animals↗
PubMed2003

The human genome and comparative genomics: understanding human evolution, biology, and medicine.

The entire 2.9-billion-letter sequence (nucleotide base pairs) of the human genome is available as a resource for scientific discovery. Some of the findings from the completion of the human genome were expected, confirming knowledge anticipated by many years of research and analysis in both human and comparative genetics. Other findings were not expected. In either case, the availability of the human genome is likely to have significant implications on basic research, clinical investigation, and ultimately the practice of medicine.

Biological Evolution↗
PubMedDate not supplied

Genomic analyses of the evolution of LGR genes.

Recent completion of the sequencing of genomes from several mammals, teleosts and invertebrates has shown that G protein-coupled receptors (GPCRs) are one of the conserved groups of cell surface receptors with an ancient origin. GPCRs play important roles in diverse physiological functions and are the most important targets for pharmaceutical discoveries. Recent work based on the search for gene with structural similarity to LH, FSH and thyroid-stimulating hormone (TSH) receptors in diverse genomes has led to the identification of a group of GPCRs called Leucine-rich repeat-containing, G protein-coupled Receptor (LGR). We present the genomic analyses of the evolution of LGR genes in the literature.

Animals↗