scholarly journals Genomic Signatures in Microbes—Properties and Applications

2011 ◽  
Vol 11 ◽  
pp. 715-725 ◽  
Author(s):  
Jon Bohlin
Keyword(s):  
Dna Sequences ◽  
Gc Content ◽  
Genomic Signature ◽  
Closely Related Species ◽  
Microbial Genomes ◽  
Genomic Signatures ◽  
A Genome ◽  
The Mean ◽  
Microbial Dna ◽  
Genomic Dna Sequence

The ratio of genomic oligonucleotide frequencies relative to the mean genomic AT/GC content has been shown to be similar for closely related species and, therefore, said to reflect a “genomic signature”. The genomic signature has been found to be more similar within genomes than between closely related genomes. Furthermore, genomic signatures of closely related organisms are, in turn, more similar than more distantly related organisms. Since the genomic signature is remarkably stable within a genome, it can be extracted from only a fraction of the genomic DNA sequence. Genomic signatures, therefore, have many applications. The most notable examples include recognition of pathogenicity islands in microbial genomes and identification of hosts from arbitrary DNA sequences, the latter being of great importance in metagenomics. What shapes the genomic signature in microbial DNA has been readily discussed, but difficult to pinpoint exactly. Most attempts so far have mainly focused on correlations fromin silicodata. This mini-review seeks to summarize possible influences shaping the genomic signature and to survey a set of applications.

scholarly journals Evolutionary dynamics of neutral phenotypes under DNA substitution models

2020 ◽  
Author(s):  
Shadi Zabad ◽  
Alan M Moses
Keyword(s):  
Dna Sequences ◽  
Evolutionary Dynamics ◽  
Gc Content ◽  
Stabilizing Selection ◽  
Restoring Force ◽  
Dna Substitution ◽  
Long Term Trends ◽  
The Mean ◽  
Molecular Phenotypes

AbstractWe study the evolution of quantitative molecular traits in the absence of selection. Using a simple theory based on Felsenstein’s 1981 DNA substitution model, we predict a linear restoring force on the mean of an additive phenotype. Remarkably, the mean dynamics are independent of the effect sizes and genotype and are similar to the widely-used OU model for stabilizing selection. We confirm the predictions empirically using additive molecular phenotypes calculated from ancestral reconstructions of putatively unconstrained DNA sequences in primate genomes. We show that the OU model is favoured by inference software even when applied to GC content of unconstrained sequences or simulations of DNA evolution. We predict and confirm empirically that the dynamics of the variance are more complicated than those predicted by the OU model, and show that our results for the restoring force of mutation hold even for non-additive phenotypes, such as number of transcription factor binding sites, longest encoded peptide and folding propensity of the encoded peptide. Our results have implications for efforts to infer selection based on quantitative phenotype dynamics as well as to understand long-term trends in evolution of quantitative molecular traits.

scholarly journals PolyCRACKER, a robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution

2018 ◽  
Author(s):  
Sean P. Gordon ◽  
Joshua J. Levy ◽  
John P. Vogel
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Related Species ◽  
Software Package ◽  
Gc Content ◽  
Individual Species ◽  
Closely Related Species ◽  
As Species ◽  
Pooled Dna ◽  
Species Specific

AbstractExisting methods for assigning sequences to individual species from pooled DNA samples rely on differences in genome properties like GC content or sequences from related species. These approaches do not work for closely related species where gross features are indistinguishable and related genomes are lacking. We describe a method and associated software package that uses rapidly evolving repetitive DNA to circumvent these limitations. By using short, repetitive, DNA sequences as species-specific signals we separated closely related genomes without any prior knowledge. This approach is ideal for separating the subgenomes of polyploid species with unsequenced or unknown progenitor genomes.

scholarly journals Analysis of Dinucleotide Bias and Genomic Signatures Across Cyanobacterial Genomes

2013 ◽  
Vol 3 (3) ◽  
pp. 265-279
Author(s):  
Dhananjaya P. Singh ◽  
Ratna Prabha
Keyword(s):  
Nucleotide Sequence ◽  
Genome Sequence ◽  
Relative Abundance ◽  
Similar Pattern ◽  
Gc Content ◽  
Marine Organisms ◽  
Genomic Signature ◽  
Genomic Signatures ◽  
Genome Wide ◽  
Dinucleotide Bias

Dinucleotide relative abundance or frequency of dinucleotides in particular nucleotide sequence is reported as genomic signature as it is specific across different DNA samples and able to identify the variance among different groups whereas identical or similar for closely related organisms. Dinucleotide relative abundance value is identified to be overall constant due to numerous factors as dinucleotide stacking energy and DNA helicity, mechanisms of replication, repair and context-dependent mutation pressures and includes information about genome-wide processes. In this study, we analyzed genome sequence of 41 cyanobacteria to gain an insight of dinucleotide bias in their genomes. Across different dinucleotides, TA is broadly underrepresented followed by CG and then AC+GT whereas; AA+TT and GC occupied a major portion of dinucleotide distribution across all cyanobacterial genomes. Underrepresentation of TA seems to be influenced by GC-content of the members as it tends to decrease when there is an increase in GC content. Members with similar GC content possess similar pattern of genomic signature. Habitats also seem to influence the dinucleotide relative abundance values of the organisms because it is suggested that marine organisms.

PCR procedures to amplify GC-rich DNA sequences of Mycobacterium bovis

2020 ◽  
Author(s):  
Nadia Assal ◽  
Min Lin
Keyword(s):  
Mycobacterium Bovis ◽  
Dna Sequences ◽  
Gc Content ◽  
Pcr Amplification ◽  
High Fidelity ◽  
Dna Templates ◽  
Technical Problems ◽  
Large Gene ◽  
A Genome ◽  
Dna Template

AbstractAmplification of high GC content genes by PCR is a major challenge during the creation of recombinant GC-rich DNA constructs. This may be due to the difficulty in DNA denaturation or the possibility of forming secondary structures from DNA templates. Tools have been described to address the technical problems associated with the amplification of shorter sequences (<1000 bp). However, obstacles of synthesizing larger-sized GC-rich sequences by PCR continue to exist. This study aims to investigate the amplification of long and high GC content genes by PCR from the Mycobacterium bovis, a genome with GC content >60%, in comparison to amplifying a gene from the Listeria monocytogenes genome, a genome with a 37.8% GC content. Three PCR protocols were designed and experimented at various conditions with two M. bovis genes, Mb0129, a large gene of 1794 bp with 77.5% GC content, mpb83, a smaller gene of 663 bp in length with moderate GC content of 63%, together with LMHCC_RS00060, a large L.monocytogenes gene of 1617 bp with a lower GC content of 41.53%. The result demonstrated the superiority of the 2-step PCR protocol over other protocols in PCR amplification of Mb0129 when specific high fidelity DNA polymerases were used in the presence of an enhancer. The study highlighted the importance of manipulating the cycling conditions to perform the annealing and extension steps at higher temperatures for a successful PCR amplification of a large GC-rich DNA template. The PCR protocols developed in this study can be valuable tools for the amplification of long GC-rich DNA sequences for various downstream applications.

The Age of Nonsynonymous and Synonymous Mutations in Animal mtDNA and Implications for the Mildly Deleterious Theory

Genetics ◽  
1999 ◽  
Vol 153 (1) ◽  
pp. 497-506 ◽  
Author(s):  
Rasmus Nielsen ◽  
Daniel M Weinreich
Keyword(s):  
Dna Sequences ◽  
Purifying Selection ◽  
Data Sets ◽  
Deleterious Mutations ◽  
Synonymous Mutations ◽  
Weak Evidence ◽  
Mitochondrial Data ◽  
The Mean ◽  
Excess Number ◽  
Neutral Mutations

Abstract McDonald/Kreitman tests performed on animal mtDNA consistently reveal significant deviations from strict neutrality in the direction of an excess number of polymorphic nonsynonymous sites, which is consistent with purifying selection acting on nonsynonymous sites. We show that under models of recurrent neutral and deleterious mutations, the mean age of segregating neutral mutations is greater than the mean age of segregating selected mutations, even in the absence of recombination. We develop a test of the hypothesis that the mean age of segregating synonymous mutations equals the mean age of segregating nonsynonymous mutations in a sample of DNA sequences. The power of this age-of-mutation test and the power of the McDonald/Kreitman test are explored by computer simulations. We apply the new test to 25 previously published mitochondrial data sets and find weak evidence for selection against nonsynonymous mutations.

Patiriella pseudoexigua (Asteroidea: Asterinidae): a cryptic species complex revealed by molecular and embryological analyses

2003 ◽  
Vol 83 (5) ◽  
pp. 1109-1116 ◽  
Author(s):  
Michael W. Hart ◽  
Maria Byrne ◽  
Sheri L. Johnson
Keyword(s):  
Dna Sequences ◽  
Original Description ◽  
Sensu Stricto ◽  
Genetic Distances ◽  
New Combination ◽  
Sea Stars ◽  
Planktonic Larva ◽  
Closely Related Species ◽  
Planktonic Larvae ◽  
Cryptic Species Complex

Cryptic lineages were identified within a morphologically uniform group of sea stars distributed from Australia to Japan. Among eight populations, all of which have been referred to Patiriella pseudoexigua, we found seven unique mitochondrial DNA sequences clustered into four distinct lineages. These four lineages formed a monophyletic group in which sister clades were separated by small genetic distances but could be differentiated from each other on the basis of reproductive differences. The four lineages thus appear to be separate but very closely related species. Examination of reproduction in several Queensland populations revealed that one population (Statue Bay) consisted of hermaphroditic intragonadal brooders with live-born offspring while other populations (Townsville, Bowen, Airlie Beach) consisted of dioecious free-spawners with a planktonic larva. The brooded larvae from central Queensland populations closely resembled brooded embryos and larvae of a Japanese lineage, while the planktonic larvae from northern Queensland were similar to the original description of planktonic larvae from a Taiwan population. However, each of the viviparous lineages was more closely related to a lineage with planktonic larval development than the viviparous lineages were to each other. Patiriella pseudoexigua thus comprises at least four species with different reproductive phenotypes in which viviparous brooding appears to have evolved in parallel. Based on previous taxonomic work we propose the following names for these four lineages: the dioecious free-spawner from northern Queensland (including the P. pseudoexigua type locality) is P. pseudoexiguasensu stricto; the viviparous brooder from central Queensland is undescribed and here referred to as Patiriella sp. nov; the dioecious free-spawner from Taiwan is temporarily referred to as Patiriella sp. (a senior name for this species may be P. pentagonus); and the hermaphrodite brooder from Japan should be raised to specific status and referred to by the new combination P. pacifica.

scholarly journals THE DNA OF CAENORHABDITIS ELEGANS

Genetics ◽  
1974 ◽  
Vol 77 (1) ◽  
pp. 95-104
Author(s):  
J E Sulston ◽  
S Brenner
Keyword(s):  
Caenorhabditis Elegans ◽  
Chemical Analysis ◽  
Dna Sequences ◽  
Base Composition ◽  
Nematode Caenorhabditis Elegans ◽  
5S Rna ◽  
Base Pairs ◽  
Small Component ◽  
E Coli ◽  
The Mean

ABSTRACT Chemical analysis and a study of renaturation kinetics show that the nematode, Caenorhabditis elegans, has a haploid DNA content of 8 x IO7 base pairs (20 times the genome of E. coli). Eighty-three percent of the DNA sequences are unique. The mean base composition is 36% GC; a small component, containing the rRNA cistrons, has a base composition of 51% GC. The haploid genome contains about 300 genes for 4s RNA, 110 for 5s RNA, and 55 for (18 + 28)S RNA.

scholarly journals VARIABILITY OF EVOLUTIONARY RATES OF DNA

Genetics ◽  
1986 ◽  
Vol 113 (4) ◽  
pp. 1077-1091
Author(s):  
John H Gillespie
Keyword(s):  
Dna Sequences ◽  
Significant Excess ◽  
Ergodic Markov Chain ◽  
The Third ◽  
Markov Chain Models ◽  
Rate Of Molecular Evolution ◽  
The Mean ◽  
Nuclear Loci ◽  
The Individual ◽  
Evolution Of Proteins

ABSTRACT A statistical analysis of DNA sequences from four nuclear loci and five mitochondrial loci from different orders of mammals is described. A major aim of the study is to describe the variation in the rate of molecular evolution of proteins and DNA. A measure of rate variability is the statistic R, the ratio of the variance in the number of substitutions to the mean number. For proteins, R is found to be in the range 0.16 &lt; R &lt; 35.55, thus extending in both directions the values seen in previous studies. An analysis of codons shows that there is a highly significant excess of double substitutions in the first and second positions, but not in the second and third or first and third positions. The analysis of the dynamics of nucleotide evolution showed that the ergodic Markov chain models that are the basis of most published formulas for correcting for multiple substitutions are incompatible with the data. A bootstrap procedure was used to show that the evolution of the individual nucleotides, even the third positions, show the same variation in rates as seen in the proteins. It is argued that protein and silent DNA evolution are uncoupled, with the evolution at both levels showing patterns that are better explained by the action of natural selection than by neutrality. This conclusion is based primarily on a comparison of the nuclear and mitochondrial results.

scholarly journals Accumulation of mutations in sexual and asexual populations

1987 ◽  
Vol 49 (2) ◽  
pp. 135-146 ◽  
Author(s):  
Pekka Pamilo ◽  
Masatoshi Nei ◽  
Wen-Hsiung Li
Keyword(s):  
Weak Selection ◽  
Population Variance ◽  
Asexual Population ◽  
Term Evolution ◽  
A Genome ◽  
Analytical Formulae ◽  
The Mean ◽  
Asexual Populations ◽  
Mutant Genes

SummaryThe accumulation of beneficial and harmful mutations in a genome is studied by using analytical methods as well as computer simulation for different modes of reproduction. The modes of reproduction examined are biparental (bisexual, hermaphroditic), uniparental (selfing, automictic, asexual) and mixed (partial selfing, mixture of hermaphroditism and parthenogenesis). It is shown that the rates of accumulation of both beneficial and harmful mutations with weak selection depend on the within-population variance of the number of mutant genes per genome. Analytical formulae for this variance are derived for neutral mutant genes for hermaphroditic, selfing and asexual populations; the neutral variance is largest in a selfing population and smallest in an asexual population. Directional selection reduces the population variance in most cases, whereas recombination partially restores the reduced variance. Therefore, biparental organisms accumulate beneficial mutations at the highest rate and harmful mutations at the lowest rate. Selfing organisms are intermediate between biparental and asexual organisms. Even a limited amount of outcrossing in largely selfing and parthenogenetic organisms markedly affects the accumulation rates. The accumulation of mutations is likely to affect the mean population fitness only in long-term evolution.

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