Related papers: r/K selection of GC content in prokaryotes
Genomes in living organisms consist of the nucleotides adenine (A), guanine (G), cytosine (C) and thymine (T). All prokaryotes have genomes consisting of double-stranded DNA, where the A's and G's (purines) of one strand bind respectively…
Genome length varies widely among organisms, from compact genomes of prokaryotes to vast and complex genomes of eukaryotes. In this study, we theoretically identify the evolutionary pressures that may have driven this divergence in genome…
We describe the distribution of Guanine and Cytosine (GC) content in the third codon position (GC3) distributions in different species, analyze evolutionary trends and discuss differences between genes and organisms with distinct GC3…
The number of available genomes of prokaryotic organisms is rapidly growing enabling comparative genomics studies. The comparison of genomes of organisms with a common phenotype, habitat or phylogeny often shows that these genomes share…
The genetic code refers to a rule that maps 64 codons to 20 amino acids. Nearly all organisms, with few exceptions, share the same genetic code, the standard genetic code (SGC). While it remains unclear why this universal code has arisen…
A model is presented relating the evolution of genomic GC content over time to AT$\rightarrow$GC and GC$\rightarrow$AT mutation rates. By employing It\^o calculus it is shown that if mutation rates in asexually reproducing organisms are…
This study presents the first global, 1 Mbp level analysis of patterns of nucleotide substitutions along the human lineage. The study is based on the analysis of a large amount of repetitive elements deposited into the human genome since…
The common understanding of protein evolution has been that neutral or slightly deleterious mutations are fixed by random drift, and evolutionary rate is determined primarily by the proportion of neutral mutations. However, recent studies…
Background: Prior to the current genomic era it was suggested that the number of protein-coding genes that an organism made use of was a valid measure of its complexity. It is now clear, however, that major incongruities exist and that…
GC-content, the ratio of guanine and cytosine bases in an entire nucleotide sequence, and palindromic sequences are unique for every organism due to genomic evolution. The goals of our research was to establish a correlation between…
Prokaryotes living at extreme environmental temperatures exhibit pronounced signatures in the amino acid composition of their proteins and nucleotide compositions of their genomes reflective of adaptation to their thermal environments.…
Across all kingdoms of biological life, protein-coding genes exhibit unequal usage of synonmous codons. Although alternative theories abound, translational selection has been accepted as an important mechanism that shapes the patterns of…
The GC-content is very variable in different genome regions and species but although many hypothesis we still do not know the reason why. Here we show that a relationship exists with the mutation rate, in particular we noticed a new…
Networks exhibiting "accelerating" growth have total link numbers growing faster than linearly with network size and can exhibit transitions from stationary to nonstationary statistics and from random to scale-free to regular statistics at…
Prokaryotic gene prediction plays an important role in understanding the biology of organisms and their function with applications in medicine and biotechnology. Although the current gene finders are highly sensitive in finding long genes,…
Much information is stored in amino acid composition of protein and base composition of DNA. We simulated the evolution of amino acid frequencies and genomic GC content by a linguistic model. It is showed that the evolution of genetic code…
The unconstrained genomic DNA of bacteria forms a coil, which volume exceeds 1000 times the volume of the cell. Since prokaryotes lack a membrane-bound nucleus, in sharp contrast with eukaryotes, the DNA may consequently be expected to…
Relation of genome sizes to organisms complexity is still described rather equivocally. Neither the number of genes (G-value), nor the total amount of DNA (C-value) correlates consistently with phenotype complexity. Using information theory…
Protein structure prediction can be shown to be an NP-hard problem; the number of conformations grows exponentially with the number of residues. The native conformations of proteins occupy a very small subset of these, hence an exploratory,…
Shaped by natural selection and other evolutionary forces, an organism's evolutionary history is reflected through its genome sequence, content of functional elements and organization. Consequently, organisms connected through phylogeny,…