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At least 19 recordsLinked to original sources
PubMed1991

Continuous distribution of Mycoplasma genome sizes.

Genome sizes of eleven strains of eight species of Mollicutes Mycoplasmataceae were investigated by pulsed-field gel electrophoresis. Mycoplasma genomic sizes were determined from the sum of the sizes of fragments obtained after digestion of genomic DNA with restriction endonucleases. The sizes of the fragments were determined by comparison of their electrophoretic mobilities with those of lambda DNA concatemers. Specific restriction endonucleases were chosen so that after digestion three to ten fragments were obtained. The values for genome size derived by this method showed a continuous distribution that ranged from approximately 650 kb for Mycoplasma hyorhinis BTS-7 to 1600 kb for Acholeplasma laidlawii FHM.

Acholeplasma laidlawii↗
PubMed2004

[The influence of transposable elements on genome size].

Genome size displays an important variability between species without any direct link to complexity. This paradox, so-called "C value paradox", now becomes understood as resulting from a differential abundance of numerous repeated sequences, among which transposable elements. Genomes indeed contain a important proportion of such sequences (95 % of DNA in man, about 45 % of which are transposable elements, up to 99 % of DNA in some plants). While most investigations until now are focalized on genes or coding sequences, which thus represent a small part of the genome, more attention now is dedicated on so-called non-coding sequences. Transposable elements, which are capable of moving around in genomes, inducing mutations, chromosomal rearrangements, gene expression regulations, thus appear as major actors in diversity and evolution. We present here a brief review of the most prominent acquisition in this expanding domain.

Animals↗
PubMed2005

Nuclear genome size and genomic distribution of ribosomal DNA in Musa and Ensete (Musaceae): taxonomic implications.

Nuclear DNA content and genomic distributions of 5S and 45S rDNA were examined in nineteen diploid accessions of the genus Musa representing its four sections Eumusa, Rhodochlamys, Callimusa and Australimusa, and in Ensete gilletii, which was the outgroup in this study. In the Eumusa (x = 11), 2C DNA content ranged from 1.130 to 1.377 pg, M. balbisiana having the lowest DNA content of all sections. M. beccarii (x = 9), a representative of Callimusa, had the highest 2C nuclear DNA content (1.561 pg). Species belonging to Rhodochlamys (x = 11) and Australimusa (x = 10) had 2C DNA contents ranging from 1.191 to 1.299 pg and from 1.435 to 1.547 pg, respectively. E. gilletii (x = 9) had 2C DNA content of 1.210 pg. The number of 5S rDNA loci in Musa varied from 4 to 8 per diploid cell. While different numbers of 5S rDNA loci were observed within Eumusa and Rhodochlamys, four 5S rDNA loci were observed in all accessions of Australimusa. M. beccarii (Callimusa) and E. gilletii contained 5S rRNA gene clusters on five and six chromosomes, respectively. The number of 45S rDNA loci was conserved within individual sections. Hierarchical cluster analysis of genome size, number of chromosomes and 45S rDNA sites suggested a close relationship between Rhodochlamys and Eumusa; Australimusa was clearly separated as were M. beccarii and E. gilletii. Within the Eumusa-Rhodochlamys group, M. balbisiana, M. schizocarpa and M. ornata formed distinct subgroups, clearly separated from the accessions of M. acuminata, M. mannii, M. laterita and M. velutina, which formed a tight subgroup. The results expand the knowledge of genome size and genomic distribution of ribosomal DNA in Musa and Ensete. They aid in clarification of the taxonomical classification of Musa and show a need to supplement the analyses on the DNA sequence level with cytogenetic studies.

Cell Nucleus↗
PubMed1990

Use of pulsed-field agarose gel electrophoresis to size genomes of Campylobacter species and to construct a SalI map of Campylobacter jejuni UA580.

To determine the physical length of the chromosome of Campylobacter jejuni, the genome was subjected to digestion by a series of restriction endonucleases to produce a small number of large restriction fragments. These fragments were then separated by pulsed-field gel electrophoresis with the contour-clamped homogeneous electric field system. The DNA of C. jejuni, with its low G+C content, was found to have no restriction sites for enzymes NotI and SfiI, which cut a high-G+C regions. Most of the restriction enzymes that were used resulted in DNA fragments that were either too numerous or too small for genome size determination, with the exception of the enzymes SalI (5' ... G decreases TCGAG ... 3'), SmaI (5' .... CCC decreases GGG .... 3'), and KpnI (5' ... GGTAC decreases C .... 3'). With SalI, six restriction fragments with average values of 48.5, 80, 110, 220, 280, and 980 kilobases (kb) were obtained when calibrated with both a lambda DNA ladder and yeast Saccharomyces cerevisiae chromosome markers. The sum of these fragments yielded an average genome size of 1.718 megabases (Mb). With SmaI, nine restriction fragments with average values ranging from 39 to 371 kb, which yielded an average genome size of 1.726 Mb were obtained. With KpnI, 11 restriction fragments with sizes ranging from 35 to 387.5 kb, which yielded an average genome size of 1.717 Mb were obtained. A SalI restriction map was derived by partial digestion of the C. jejuni DNA. The genome sizes of C. laridis, C. coli, and C. fetus were also determined with the contour-clamped homogeneous electric field system by SalI, SmaI, and KpnI digestion. Average genome sizes were found to be 1.714 Mb for C. coli, 1.267 Mb for C. fetus subsp. fetus, and 1.451 Mb for C. laridis.

Base Sequence↗
PubMed1990

Human ureaplasmas show diverse genome sizes by pulsed-field electrophoresis.

Contour clamped homogeneous field (CHEF) agarose gel electrophoresis (AGE), ramped to give linear separation of DNA molecules of 600-1600 kilobase pairs (kbp), was used to determine mobilities for full-sized genomic DNA of the serotype standard strains of the human genital mollicutes, Ureaplasma urealyticum relative to yeast chromosomal DNA markers. Indicated genome sizes (in kbp) were 760 for the four biotype 1 strains and 840-1140 for eleven biotype 2 strains. Other estimates were: 720 for Mycoplasma hominis, 1070 for Mycoplasma hyopneumoniae, 890 for Mycoplasma flocculare, 1180 and 1350 for Mycoplasma mycoides subsp. mycoides Y and GC1176-2, respectively, and 1650 and 1580 for Acholeplasma laidlawii B and PG 8, respectively. These data supplement previous evidence from CHEF AGE that the genomes of the Mycoplasmataceae are diverse in size with some larger than previously estimated from DNA renaturation kinetics.

DNA, Bacterial↗
PubMed1999

Random amplified polymorphic DNA analysis, genome size, and genomic in situ hybridization of triploid viviparous onions

Triploid viviparous onions (Allium cepa L. var. viviparum Metzg. (ALEF.), auct.), (2n = 3x = 24), are known in some countries only as a rare relic crop, while in other parts of the world they are still traditionally or even commercially cultivated. Results indicating an identical random amplified polymorphic DNA (RAPD) banding pattern and the same DNA content (2C = 43.4 pg) establish the high genetic similarity and the unique origin of the Croatian clone Ljutika and the Indian clone Pran. In order to determine the parental Allium species of these natural triploid hybrids, genomic fluorescent in situ hybridization (GISH) was applied. Biotinylated genomic DNAs from six diploid Allium species (A. cepa L., A. fistulosum L., A. roylei Stearn, A. vavilovii M. Pop. et Vved., A. galanthum Kar. et Kir., A. oschaninii O. Fedtsch.) were used as probes in this study. While probes obtained from genomic DNA of A. cepa, A. vavilovii, and A. roylei hybridized to somatic chromosomes of Ljutika probes from A. fistulosum, A. galanthum, and A. oschaninii did not. The DNA probes of A. cepa and A. roylei each completely or predominantly labelled one genome (eight chromosomes). A few chromosomes, the markers of the triploid karyotype, were not completely labelled by any probe applied. Our GISH results indicate that triploid viviparous onions might possess a complex triparental genome organization.

Journal Article↗
PubMed1981

Reexamination of the genome size of myxobacteria, including the use of a new method for genome size analysis.

The genome sizes of two myxobacteria, Myxococcus xanthus and Stigmatella aurantiaca, were measured by renaturation analysis and also by a new method involving the quantitation of individual restriction fragments. In contrast to several previous reports, which indicate that M. xanthus has a genome size which is three to four times that of Escherichia coli, the present measurements indicated that the M. xanthus genome is only about 24 to 53% larger than that of E. coli. S. aurantiaca had a genome size nearly identical to that of M. xanthus. Of possible significance is the fact that the renaturation curves of M. xanthus and S. aurantiaca deoxyribonucleic acid both exhibited significant fractions which renatured with rapid, unimolecular kinetics. However, we were unable to establish that these fractions represented inverted repeats of repetitive sequences.

Chromosomes, Bacterial↗
PubMed2025

Complexity of schistosome vector bulinine snails in Kenya: Insights from nuclear genome size variation, complete mitochondrial genome sequence, and morphometric analysis.

Investigations of nuclear genome size, complete mitochondrial genome (mitogenome) sequence, and morphometrics were conducted on specimens of Bulinus snails (Gastropoda: Planorbidae) collected from 14 locations across the east coast, central Kenya, and western Kenya around the Lake Victoria region (November 2013 and January 2024). Flow cytometry measurements of DNA content (C-value) revealed unexpected variation in nuclear genome size, with diploid Bulinus africanus and B. forskalii species groups showing C-values ranging from 0.76 to 1.98 pg, while tetraploid B. truncatus had a C-value of 1.82 pg. Additionally, C-values for six B. globosus specimens from different localities ranged from 1.43 to 1.98 pg. These findings suggest that bulinine snails, particularly the B. africanus species group, have undergone genome expansion, whole genome duplication (polyploidization), or both, which have not been previously recognized. Next-generation sequencing was performed to determine and annotate 14 complete mitogenome sequences. Despite the well-conserved arrangement of protein-coding genes, two versions of mtDNA genome structure, distinguished by the tRNA-D (Asp) location, were found, designated as DCF (Asp-Cys-Phe) type (in the B. forskalii group and the B. truncatus/tropicus complex) and CF (Cys-Phe) type (in the B. africanus group). Phylogenetic analyses based on complete mtDNA sequences of bulinines from Kenya, along with cytochrome c oxidase subunit I (COX1) sequences from various localities across Africa, contributed to resolving species identities and provided further support for the presence of multiple or cryptic species in the taxon B. globosus. A landmark-based morphometric analysis was ineffective in distinguishing these species. This study reveals unexpected nuclear genome size variation, provides new mitogenome sequences, and highlights the limitations of morphological analysis. It offers valuable insights into the cytogenetics, polyploidy, genomics, taxonomy, and evolution of bulinines, which serve as intermediate hosts for schistosomes responsible for human urogenital schistosomiasis and intestinal schistosomiasis in domestic and wild mammals.

Animals↗
PubMed2000

Evidence for DNA loss as a determinant of genome size.

Eukaryotic genome sizes range over five orders of magnitude. This variation cannot be explained by differences in organismic complexity (the C value paradox). To test the hypothesis that some variation in genome size can be attributed to differences in the patterns of insertion and deletion (indel) mutations among organisms, this study examines the indel spectrum in Laupala crickets, which have a genome size 11 times larger than that of Drosophila. Consistent with the hypothesis, DNA loss is more than 40 times slower in Laupala than in Drosophila.

Animals↗
PubMed2004

Trends between gene content and genome size in prokaryotic species with larger genomes.

Although the evolution process and ecological benefits of symbiotic species with small genomes are well understood, these issues remain poorly elucidated for free-living species with large genomes. We have compared 115 completed prokaryotic genomes by using the Clusters of Orthologous Groups database to determine whether there are changes with genome size in the proportion of the genome attributable to particular cellular processes, because this may reflect both cellular and ecological strategies associated with genome expansion. We found that large genomes are disproportionately enriched in regulation and secondary metabolism genes and depleted in protein translation, DNA replication, cell division, and nucleotide metabolism genes compared to medium- and small-sized genomes. Furthermore, large genomes do not accumulate noncoding DNA or hypothetical ORFs, because the portion of the genome devoted to these functions remained constant with genome size. Traits other than genome size or strain-specific processes are reflected by the dispersion around the mean for cell functions that showed no correlation with genome size. For example, Archaea had significantly more genes in energy production, coenzyme metabolism, and the poorly characterized category, and fewer in cell membrane biogenesis and carbohydrate metabolism than Bacteria. The trends we noted with genome size by using Clusters of Orthologous Groups were confirmed by our independent analysis with The Institute for Genomic Research's Comprehensive Microbial Resource and Kyoto Encyclopedia of Genes and Genomes' Orthology annotation databases. These trends suggest that larger genome-sized species may dominate in environments where resources are scarce but diverse and where there is little penalty for slow growth, such as soil.

Animals↗
PubMed2002

Evolution of genome size in Drosophila. is the invader's genome being invaded by transposable elements?

Genome size varies considerably between species, and transposable elements (TEs) are known to play an important role in this variability. However, it is far from clear whether TEs are involved in genome size differences between populations within a given species. We show here that in Drosophila melanogaster and Drosophila simulans the size of the genome varies among populations and is correlated with the TE copy number on the chromosome arms. The TEs embedded within the heterochromatin do not seem to be involved directly in this phenomenon, although they may contribute to differences in genome size. Furthermore, genome size and TE content variations parallel the worldwide colonization of D. melanogaster species. No such relationship exists for the more recently dispersed D. simulans species, which indicates that a quantitative increase in the TEs in local populations and fly migration are sufficient to account for the increase in genome size, with no need for an adaptation hypothesis.

Animals↗
PubMed1998

[Precise DNA cytometry: investigation of individual variability in animal genome size].

The variability of genome size was studied in animal populations and in cell populations of different animal species by means of DNA flow cytometry with the precision level of several tenths of percent. For populations of frog Rana esculenta and laboratory mouse lines C57B1 and CBA the analysis was made with cells of different tissues: erythrocytes for R. esculenta, splenocytes for mice and haploid cells of testes for both species. The results of DNA cytometry, obtained with cells of different species, were shown to be correlated, which indicates the objectivity of individual intrapopulation differences in the genome size recorded with DNA flow cytometry. The level of variability (expressed as CV) was 0.3-0.4% for the population of frogs, and 0.2-0.3% for mouse lines. The analysis of genome size variability in cell populations of different animal species revealed a relationship between the variability level and the genome size: the coefficient of variance of the peak of DNA histogram was inversely related to the square root of genome size. The latter effect may be explained by fluctuations of a measured multicomponent object, but it is still unclear whether these fluctuations could be related to the genome size or to pecularities of chromatin structure. It is concluded that the method of flow DNA cytometry may be effective for studying individual differences in the genome size.

Animals↗
PubMedDate not supplied

The bigger the C-value, the larger the cell: genome size and red blood cell size in vertebrates.

Vertebrate genome sizes vary roughly 350-fold and correlate with a variety of cellular and organismal parameters. Most notable among these is the relationship between genome size ("C-value") and red blood cell (RBC) size, which can be identified within and among each of the five vertebrate classes. This relationship, in turn, leads to important associations between genome size and features such as metabolic rate (at least in homeotherms). The present article describes the correlation between genome size and RBC size in vertebrates and discusses some of the cytological, physiological, and evolutionary implications of this relationship.

Animals↗
PubMed2002

Genome size and microsatellites: the effect of nuclear size on amplification potential.

Although the frequency of microsatellite DNA regions generally increases with increasing genome size, genome size has a negative effect on polymerase chain reaction (PCR) amplification. Thus, researchers developing sets of PCR primers, as is commonly done for microsatellite DNA regions, may encounter greater difficulty when working with species that have larger genomes. I investigated the effect of genome size on overall amplification success using data from nine different metazoan taxa. The proportion of primer sets that did not amplify PCR products was strongly and positively correlated with the haploid C value of the target species. Increasing genome size may affect amplification success negatively because of a decrease in target:nontarget DNA or by dilution of the available primer pool by nonspecific binding.

Animals↗
PubMed2002

Genome size and developmental complexity.

Haploid genome size (C-value) is correlated positively with cell size, and negatively with cell division rate, in a variety of taxa. Because these associations are causative, genome size has the potential to impact (and in turn, be influenced by) organism-level characters affected by variation in either of these cell-level parameters. One such organismal feature is development. Developmental rate, in particular, has been associated with genome size in numerous plant, vertebrate, and invertebrate groups. However, rate is only one side of the developmental coin; the other important component is complexity. When developmental complexity is held essentially constant, as among many plants, developmental rate is the visibly relevant parameter. In this case, genome size can impose thresholds on developmental lifestyle (and vice versa), as among annual versus perennial plants. When developmental rate is constrained (as during time-limited amphibian metamorphosis), complexity becomes the notable variable. An appreciation for this rate-complexity interaction has so far been lacking, but is essential for an understanding of the relationships between genome size and development. Moreover, such an expanded view may help to explain patterns of variation in taxa as diverse as insects and fish. In each case, a hierarchical approach is necessary which recognizes the complex interaction of evolutionary processes operating at several levels of biological organization.

Amphibians↗
PubMed2002

Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis.

Genome size varies greatly across angiosperms. It is well documented that, in addition to polyploidization, retrotransposon amplification has been a major cause of genome expansion. The lack of evidence for counterbalancing mechanisms that curtail unlimited genome growth has made many of us wonder whether angiosperms have a "one-way ticket to genomic obesity." We have therefore investigated an angiosperm with a well-characterized and notably small genome, Arabidopsis thaliana, for evidence of genomic DNA loss. Our results indicate that illegitimate recombination is the driving force behind genome size decrease in Arabidopsis, removing at least fivefold more DNA than unequal homologous recombination. The presence of highly degraded retroelements also suggests that retrotransposon amplification has not been confined to the last 4 million years, as is indicated by the dating of intact retroelements.

Arabidopsis↗
PubMed2002

Mutational equilibrium model of genome size evolution.

The paper describes a mutational equilibrium model of genome size evolution. This model is different from both adaptive and junk DNA models of genome size evolution in that it does not assume that genome size is maintained either by positive or stabilizing selection for the optimum genome size (as in adaptive theories) or by purifying selection against too much junk DNA (as in junk DNA theories). Instead the genome size is suggested to evolve until the loss of DNA through more frequent small deletions is equal to the rate of DNA gain through more frequent long insertions. The empirical basis for this theory is the finding of a strong correlation and of a clear power-function relationship between the rate of mutational DNA loss (per bp) through small deletions and genome size in animals. Genome size scales as a negative 1.3 power function of the deletion rate per nucleotide. Such a relationship is not predicted by either adaptive or junk DNA theories. However, if genome size is maintained at equilibrium by the balance of mutational forces, this empirilical relationship can be readily accommodated. Within this framework, this finding would imply that the rate of DNA gain through large insertions scales up a quarter-power function of genome size. On this view, as genome size grows, the rate of growth through large insertions is increasing as a quarter power function of genome size and the rate of DNA loss through small deletions increases linearly, until eventually, at the stable equilibrium genome size value, rates of growth and loss equal each other. The current data also suggest that the long-term variation is genome size in animals is brought about to a significant extent by changes in the intrinsic rates of DNA loss through small deletions. Both the origin of mutational biases and the adaptive consequences of such a mode of evolution of genome size are discussed.

Base Sequence↗