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PubMed1990

Compositional transitions in the nuclear genomes of cold-blooded vertebrates.

The compositional properties of DNAs from 122 species of fishes and from 18 other cold-blooded vertebrates (amphibians and reptiles) were compared with those from 10 warm-blooded vertebrates (mammals and birds) and found to be substantially different. Indeed, DNAs from cold-blooded vertebrates are characterized by much lower intermolecular compositional heterogeneities and CsCl band asymmetries, by a much wider spectrum of modal buoyant densities in CsCl, by generally lower amounts of satellites, as well as by the fact that in no case do buoyant densities reach the high values found in the GC-richest components of DNAs from warm-blooded vertebrates. In the case of fish genomes, which were more extensively studied, different orders were generally characterized by modal buoyant densities that were different in average values as well as in their ranges. In contrast, different families within any given order were more often characterized by narrow ranges of modal buoyant densities, and no difference in modal buoyant density was found within any single genus (except for the genus Aphyosemion, which should be split into several genera). The compositional differences that were found among species belonging to different orders and to different families within the same order are indicative of compositional transitions, which were shown to be essentially due to directional base substitutions. These transitions were found to be independent of geological time. Moreover, the rates of directional base substitutions were found to be very variable and to reach, in some cases, extremely high values, that were even higher than those of silent substitutions in primates. The taxonomic and evolutionary implications of these findings are discussed.

Amphibians↗
PubMed2005

The compositional transition of vertebrate genomes: an analysis of the secondary structure of the proteins encoded by human genes.

Fluctuations and increments of both C(3) and G(3) levels along the human coding sequences were investigated comparing two sets of Xenopus/human orthologous genes. The first set of genes shows minor differences of the GC(3) levels, the second shows considerable increments of the GC(3) levels in the human genes. In both data sets, the fluctuations of C(3) and G(3) levels along the coding sequences correlated with the secondary structures of the encoded proteins. The human genes that underwent the compositional transition showed a different increment of the C(3) and G(3) levels within and among the structural units of the proteins. The relative synonymous codon usage (RSCU) of several amino acids were also affected during the compositional transition, showing that there exists a correlation between RSCU and protein secondary structures in human genes. The importance of natural selection for the formation of isochore organization of the human genome has been discussed on the basis of these results.

Animals↗
PubMed1988

The effects of guanine and cytosine variation on dinucleotide frequency and amino acid composition in the human genome.

One hundred twelve human DNA sequences were analyzed with respect to dinucleotide frequency and amino acid composition. The variation in guanine and cytosine (G + C) content revealed: (1) at 2-3 and 3-1 doublet positions CG discrimination is attenuated at high G + C, but TA disfavor is enhanced, and (2) several amino acids are subject to G + C change. These findings have been reported in part for collections of sequences from various species. The present study confirms that in a single organism--the human--the G + C effects do exist. Aspects of the argument that connects G + C with protein thermal stability are also discussed.

Animals↗
PubMed2003

Compositional features of eukaryotic genomes for checking predicted genes.

Gene prediction relies on the identification of characteristic features of coding sequences that distinguish them from non-coding DNA. The recent large-scale sequencing of entire genomes from higher eukaryotes, in conjunction with currently used gene prediction algorithms, has provided an abundance of putative genes that can now be analysed for their compositional properties. Strong, systematic differences still exist, in several species, between the compositional properties of sets of ex novo predicted genes and genes that have been experimentally detected and/or verified. This is particularly evident in the estimated gene set (>45,000 genes) of the recently sequenced rice genome, where roughly half the predicted genes are compositionally unusual and have no known orthologues in the dicot Arabidopsis. In a few cases such differences might suggest a bias in experimental gene-finding protocols, but the quasi-random nature of the compositionally aberrant predicted genes is a strong indication that many, if not most, of them are false positives. It therefore appears that some important features of coding regions have not yet been taken into account in existing gene prediction programs. Statistical base compositional properties of curated gene data sets from vertebrates, which we briefly review here, should therefore provide a useful benchmark for fine-tuning probabilistic gene models and model parameters that are currently in use.

Animals↗
PubMed2005

Compositional properties of green-plant plastid genomes.

We studied variation of GC contents among plastid (Pt) genomes of green plants. In the green plants, the GC contents of the whole Pt genomes range from 42.14 to 28.81%. These values are similar to those observed in the mitochondrial (Mt) genomes of the green plants, however, the GC contents in the Pt genomes are not related to those in the Mt genomes or the nuclear (Nc) genomes. In addition, some compositional properties of the three types of genomes are different. Thus, it is suggested that the GC contents of the Pt genomes are maintained independently of the other genomes within a cell. We found that the compositional bias toward AT is strong at the third codon position and in intergenic spacer (IGS) regions in the Pt genomes, and the GC contents (GC3 and GCIGS) at these sites are generally similar within each genome. Additionally, the GC3 and GCIGS are strongly related to the whole-genome GC content. Therefore, the interspecific variation of the GC contents in the Pt genomes is suggested to be mainly caused by the variation of the GC3 and GCIGS, both of which are considered to be under weak selective constraints. Using a maximum likelihood approach, we estimated equilibrium GC3 (eqGC(3)) of 12 genes in the land-plant Pt genomes. We found an increase in eqGC(3) after the divergence of liverworts. These results suggest that genome-wide factors such as GC mutational bias are important for the biased base composition in the Pt genomes.

Chlorophyta↗
PubMed1988

Compositional compartmentalization and compositional patterns in the nuclear genomes of plants.

We report here results which indicate (i) that the nuclear genomes of angiosperms is characterized by a compositional compartmentalization and an isochore structure; and (ii) that the nuclear genomes of some Gramineae exhibit strikingly different compositional patterns compared to those of many dicots. Indeed, the compositional distribution of nuclear DNA molecules (in the 50-100 Kb size range) from three dicots (pea, sunflower and tobacco) and three monocots (maize, rice and wheat) were found to be centered around lower (41%) and higher (45% for rice, 48% for maize and wheat) GC levels, respectively (and to trail towards even higher GC values in maize and wheat). Experiments on gene localization in density gradient fractions showed a remarkable compositional homogeneity in vast (greater than 100-200 Kb) regions surrounding the genes. On the other hand, the compositional distribution of coding sequences (GenBank and literature data) from dicots (several orders) was found to be narrow, symmetrical and centered around 46% GC, that from monocots (essentially barley, maize and wheat) to be broad, asymmetrical and characterized by an upward trend towards high GC values, with the majority of sequences between 60 and 70% GC. Introns exhibited a similar compositional distribution, but lower GC levels, compared to exons from the same genes.

Cell Nucleus↗
PubMed1994

Nucleotide composition as a driving force in the evolution of retroviruses.

All complete retrovirus sequences in the GenEMBL database were examined with the goal of assessing possible relationships between the nucleotide composition of retroviral genomes, the amino acid composition of retroviral proteins, and evolutionary strategies used by retroviruses. The results demonstrated that the genome of each viral lineage has a characteristic base composition and that the variations between groups are related to retroviral phylogeny. By analogy to microbial species, we suggest that the variations arise from group-specific patterns of directional mutations where the bias can be exerted on any of the four nucleotides. It is most likely that the mutational patterns are introduced during reverse transcription, and a direct participation of reverse transcriptase in the process is suspected. A straightforward strategy was used to analyze the compositional relationship between nucleotides and encoded amino acids. The procedure entailed calculations of amino acid frequencies from nucleotide content and the comparison of the calculated values to the observed amino acid frequencies in retroviruses. The results revealed an excellent correspondence between variation in genomic base composition and variation in amino acid composition of proteins with the compositional differences extending into all major coding regions of the viruses. Because of the magnitude and dispersion of these effects, and because of the nonconservative nature of many of the substitutions between groups with different genomic biases, we suggest that the variations in protein composition driven by biased nucleotide frequencies are an important factor in shaping the characteristic phenotypes of the different viral lineages. A clue to the nature of the evolutionary forces that are responsible for the generation of nucleotide biases was provided by the observation that viruses with radically different base frequencies most often inhabit the same cell type. This observation, along with analysis of amino acid and nucleotide replacement patterns between and within reverse transcriptase sequences from the various groups, permitted us to advance a model for the evolution of retroviruses. According to the model, speciation could initiate when daughter virions from a single progenitor vary in the direction of their mutational bias. These variations would exert a pleiotropic effect on the frequencies of nucleotides in all viral genes and consequently on the frequencies of amino acids in the encoded proteins. The variants with the most extreme compositional differences would have a selective advantage because their different precursor requirements would enable them to occupy different ecological niches within a single cell.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed2006

Euchromatin and pericentromeric heterochromatin: comparative composition in the tomato genome.

Eleven sequenced BACs were annotated and localized via FISH to tomato pachytene chromosomes providing the first global insights into the compositional differences of euchromatin and pericentromeric heterochromatin in this model dicot species. The results indicate that tomato euchromatin has a gene density (6.7 kb/gene) similar to that of Arabidopsis and rice. Thus, while the euchromatin comprises only 25% of the tomato nuclear DNA, it is sufficient to account for approximately 90% of the estimated 38,000 nontransposon genes that compose the tomato genome. Moreover, euchromatic BACs were largely devoid of transposons or other repetitive elements. In contrast, BACs assigned to the pericentromeric heterochromatin had a gene density 10-100 times lower than that of the euchromatin and are heavily populated by retrotransposons preferential to the heterochromatin-the most abundant transposons belonging to the Jinling Ty3/gypsy-like retrotransposon family. Jinling elements are highly methylated and rarely transcribed. Nonetheless, they have spread throughout the pericentromeric heterochromatin in tomato and wild tomato species fairly recently-well after tomato diverged from potato and other related solanaceous species. The implications of these findings on evolution and on sequencing the genomes of tomato and other solanaceous species are discussed.

Centromere↗
PubMed1998

Distinct frequency-distributions of homopolymeric DNA tracts in different genomes.

The unusual base composition of the genome of the human malaria parasite Plasmodium falciparum prompted us to systematically investigate the occurrence of homopolymeric DNA tracts in the P. falciparum genome and, for comparison, in the genomes of Homo sapiens , Saccharomyces cerevisiae , Caenorhabditis elegans , Arabidopsis thaliana , Escherichia coli and Mycobacterium tuberculosis. Comparison of theobserved frequencies with the frequencies as expected for random DNA revealed that homopolymeric (dA:dT) tracts occur well above chance in the eukaryotic genome. In the majority of these genomes, (dA:dT) tract overrepresentation proved to be an exponential function of the tract length. (dG:dC) tract overrepresentation was absent or less pronounced in both prokaryotic and eukaryotic genomes. On the basis of our results, we propose that homopolymeric (dA:dT) tracts are expanded via replication slippage. This slippage-mediated expansion does not operate on tracts with lengths below a critical threshold of 7-10 bp.

Animals↗
PubMed2002

Compositional patterns in reptilian genomes.

Sauropsids form a complex group of vertebrates including squamates (lizards and snakes), turtles, crocodiles, sphenodon and birds (which are often considered as a separate class). Although avian genomes have been relatively well studied, the genomes of the other groups have remained only sparsely characterized. Moreover, the nuclear sequences available in databanks are still very limited. In the present study, we have analysed the compositional patterns, i.e. the GC (molar fraction of guanine and cytosine in DNA) distributions, of 31 reptilian (particularly snake) genomes by analytical ultracentrifugation of DNAs in CsCl gradients. The profiles were characterized by their modal buoyant density rho(o), mean buoyant density < rho>, asymmetry < rho>- rho(o), and heterogeneity H. The modal buoyant density distribution of reptilian DNAs clearly distinguishes two groups. The snakes fall in the same range of modal densities as most mammals, whereas crocodiles, turtles and lizards show higher values (>1.700 g/cm(3)). As far as the more important compositional properties of asymmetry and heterogeneity are concerned, previous studies showed that amphibians and fishes share relatively low values, whereas birds and mammals are characterized by highly heterogeneous and asymmetric patterns (with the exception of Muridae, which have a lower heterogeneity). The present results show that the snake genomes cover a broad range of asymmetry and heterogeneity values, whereas the genomes of crocodiles and turtles cover a narrow range that is intermediate between those of fishes/amphibians and those of mammals/birds.

Animals↗
PubMed2006

Insect mitochondrial genomics 2: The complete mitochondrial genome sequence of a giant stonefly, Pteronarcys princeps, asymmetric directional mutation bias, and conserved plecopteran A+T-region elements.

Mitochondrial (mt) genome sequences of insects are receiving renewed attention in molecular phylogentic studies, studies of mt-genome rearrangement, and other unusual molecular phenomena, such as translational frameshifting. At present, the basal neopteran lineages are poorly represented by mt-genome sequences. Complete mt-genome sequences are available in the databases for only the Orthoptera and Blatteria; 9 orders are unrepresented. Here, we present the complete mt-genome sequence of a giant stonefly, Pteronarcys princeps (Plecoptera; Pteronarcyidae). The 16,004 bp genome is typical in its genome content, gene organisation, and nucleotide composition. The genome shows evidence of strand-specific mutational biases, correlated with the time between the initiation of leading and the initiation of lagging strand replication. Comparisons with other insects reveal that this trend is seen in other insect groups, but is not universally consistent among sampled mt-genomes. The A+T region is compared with that of 2 stoneflies in the family Peltoperlidae. Conserved stem-loop structures and sequence blocks are noted between these distantly related families.

Animals↗
PubMed2004

Nitrogen versus carbon use in prokaryotic genomes and proteomes.

There is growing recognition that the elemental composition of genomes and proteins can be related to resource limitation. We examine the possibility that the elemental composition of nucleic acids and the amino acids (and proteins) they encode are correlated. We report a positive association between the stoichiometric ratio of N/C content of individual amino acids and their codons. Potentially, this is an outcome of chemical interactions between amino acids and anticodons that influenced the evolution of the genetic code. We also find a strong, positive relationship between N/C values of whole genomes and proteomes, across 94 prokaryotic species. This relationship is part of a spectrum in nitrogen versus carbon use across genomes and proteomes, which is correlated with genomic GC content. GC content is correlated positively with average nitrogen use, and negatively with average carbon use, across both genomes and proteomes.

Amino Acids↗
PubMed1990

Evidence for a composite phylogenetic origin of the plastid genome of the brown alga Pylaiella littoralis (L.) Kjellm.

The nucleotide sequence and the 5' flanking region of the rbcL gene coding for the large subunit of ribulose bisphosphate-1,5-carboxylase/oxygenase of Pylaiella littoralis, a brown alga, has been determined and the deduced amino-acid sequence has been compared to those of various photosynthetic and chemoautotrophic Eubacteria, of a red alga and of green plastids (Euglena gracilis, green algae and higher plants). Unlike the rbcL genes of green plastids which are more closely related to those of cyanobacteria, the P. littoralis rbcL gene is more closely related to that of a beta-purple bacterium, as was found for the rbcS gene of another chromophytic alga [Boczar et al., Proc Natl Acad Sci USA 86: 4996-4999, 1989]. Matrix data of homology between the rbcL gene of P. littoralis and the same gene of other organisms are presented. Based on our previous report, the gene coding for the 16S rRNA from P. littoralis is closely related to that of E. gracilis (Markowicz et al., Curr Genet 14: 599-608, 1988). We suggest that the large plastid DNA molecule of P. littoralis is a phylogenetically composite genome which probably resulted from mixed endosymbiosis events, or from a horizontal transfer of DNA.

Amino Acid Sequence↗
PubMed2005

Correlations between genomic GC levels and optimal growth temperatures: some comments.

Regarding the existence of any specific correlation between optimal growth temperature and genomic GC levels, Musto et al. [FEBS Lett. 573 (2004) 73] have recently performed analysis on 20 prokaryotic families and showed that in most of the families there exists a positive correlation between these two parameters. On the basis of these results they claimed that optimal growth temperature is one of the factors that influence genomic GC composition in prokaryotes. In a subsequent article, Marashi and Ghalanbor [Biochem. Biophys. Res. Commun. 325 (2004) 381] have demonstrated that the correlation values change substantially when very few points in some of the families were excluded from the data set of Musto et al. [FEBS Lett. 573 (2004) 73]. But Marashi and Ghalanbor have not provided any reason behind this. The points excluded by Marashi and Ghalanbor are actually the outliers in the data set, which strongly affect the correlation coefficients. But the presence of outliers in large data set hardly had any effect on the correlation values. Marashi and Ghalanbor have excluded points from only those families that have small sample sizes and observed a substantial change in correlation coefficient values. Therefore, we argue that any conclusion drawn for a small sample size having outliers is always questionable. Although Musto's approach is a novel one, but to make any generalization one needs to be careful about the flawlessness in the data set.

Base Composition↗
PubMed2004

Short-range compositional correlation in the yeast genome depends on transcriptional orientation.

This article reports an analysis of composition of about 5000 intergenic regions and neighboring ORFs in the nuclear genome of Saccharomyces cerevisiae, and their correlation. Intergenic regions flanked by divergently transcribed ORFs are GC richer (36%) than those separating convergent ORFs (29%). This difference in GC content cannot be fully attributed to its location upstream or downstream the ORFs, since no such strong compositional bias is found within 3' and 5' segments of intergenic regions between ORFs transcribed in the same direction. We have also found that the GC content of intergenic regions is positively correlated to that of its flanking ORFs in tandem and divergent orientations, but not in convergent orientations, and that the correlation coefficient between the GC content of nearby ORFs is higher for divergent pairs. Our observations are discussed in the light of recent work stressing the relationships between base composition, chromatin structure and meiotic recombination.

Base Composition↗
PubMed2003

Genome size and base composition of five Pinus species from the Balkan region.

The 2C DNA content and base composition of five Pinus (2 n=24) species and two Pinus subspecies from the Balkan region have been estimated by flow cytometry. P. heldreichii (five populations) and P. peuce (one population) were assessed for the first time, as also were subspecies of P. nigra (three populations-two of subspecies nigra and one of subspecies dalmatica) along with P. sylvestris, and P. mugo from the same region. The 2C DNA values of these Pinus ranged from 42.5 pg to 54.9 pg (41.7-53.8 x 10(9)bp), and the base composition was quite stable (about 39.5% GC). Significant differences were observed between two subspecies of P. nigra and even between two populations of subsp. nigra. The two other species (P. sylvestris and P. mugo) had 2C values of 42.5 pg and 42.8 pg, respectively, while that of P. peuce was 54.9 pg. These genome sizes are in accordance with published values except for P. sylvestris, which was 20% below estimates made by other authors.

Base Composition↗
PubMed2025

De Novo Whole Genome Assemblies of Unusual Case-Making Caddisflies (Trichoptera) Highlight Genomic Convergence in the Composition of the Major Silk Gene (h-fibroin).

Trichoptera (caddisflies) is one of the most species-rich orders of aquatic insects. Species of caddisflies cover a broad ecological diversity as exemplified by various uses of underwater silk secretions. Diversity of silk use generally aligns with the evolution of major caddisfly lineages, specifically at the subordinal level: Annulipalpia (retreat makers) and Integripalpia (cocoon and tube-case makers). However, silk use within suborders differs for a few exceptional species in these clades. In this study, we provide the first whole genome assemblies and annotations for two unusual Integripalpia species: Limnocentropus insolitus, whose hard tube-case is anchored to boulders by a rigid, elongated silken stalk, and Phryganopsyche brunnea which builds a "floppy" cylindrical case that lacks the typical robustness of tube-cases. Its texture rather resembles that of the flexible retreats built by Annulipalpia. Using the two high-quality genome assemblies, we identified and annotated the major silk gene, h-fibroin, and compared its amino acid composition across various groups, including retreat, cocoon, and tube-case makers. Our phylogenetic analysis confirmed the phylogenetic position of the two species in the tube-case-making clade. The major silk gene of L. insolitus shows a similar amino acid composition to other tube-case-making species. In contrast, the amino acid composition of P. brunnea resembles that of retreat-making species, in particular with regard to the high content of proline. This is consistent with the hypothesis that proline could be linked to enhanced extensibility of silk fibers. Taken together, our results underscore the role of silk genes in shaping the evolutionary ecology of retreat- and tube-case-making in caddisflies.

Animals↗
PubMed1998

Mutation pressure, natural selection, and the evolution of base composition in Drosophila.

Genome sequencing in a number of taxa has revealed variation in nucleotide composition both among regions of the genome and among functional classes of sites in DNA. Mutational biases, biased gene conversion, and natural selection have been proposed as causes of this variation. Here, we review patterns of base composition in Drosophila DNA. Nucleotide composition in Drosophila melanogaster varys regionally, and base composition is correlated between introns and exons. Drosophila species also show striking patterns of non-random codon usage. Patterns of synonymous codon usage and the biochemistry of translation suggest that natural selection may act at 'silent' sites. A relationship between recombination rates and codon usage and comparisons of the evolutionary dynamics of silent mutations within and between species support natural selection discriminating among synonymous codons. The causes of regional base composition variation are less clear. Progress in functional studies of non-coding DNA, further investigations of genome patterns, and statistical tests based on evolutionary theory will lead to a greater understanding of the contributions of mutational processes and natural selection in patterning genome-wide nucleotide composition.

Animals↗