background: most of the amino acids are encoded by more than one codon, termed as synonymous codons. synonymous codon usage is not random as it is unique to species. in each amino acid family, some synonymous codons are preferred and this is referred to as synonymous codon usage bias (scub). trends associated with evolution of scub and factors influencing its diversification in plastomes of gen...

Heterogeneities in nucleotide content distribution along the length of Zaire ebolavirus and Marburg virus genomes have been analyzed. Results showed that there is asymmetric mutational A-pressure in the majority of Zaire ebolavirus genes; there is mutational AC-pressure in the coding region of the matrix protein VP40, probably, caused by its high expression at the end of the infection process; ...

1. Abstract 2. Introduction 2.1. Definition: purification versus complementation 2.2. Mutations 3. Some computer models 3.1. Emerging complementarity 3.2. Gamete recognition 3.3. Role of mutational pressure on the emerging of complementarity 3.4. The role of inbreeding 4. Consequences 4.1. Sympatric speciation 4.2. Distribution of recombination events 4.3. Effect of gamete recognition 5. Discus...

Directional mutational pressure associated with replication is one of the most significant forces shaping structure of bacterial genomes and influencing the evolution of their genes. Here we introduced the model of bacterial genome evolution including two mutational pressures acting in differently replicated DNA strands (leading and lagging). The simulations were performed on the population of ...

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We have used the Monte Carlo method for simulating the evolution of protein coding sequences from the Borrelia burgdorferi genome under the directional mutational pressure, described by the nucleotide substitution matrix experimentally found for this genome. Since the mutational pressure is asymmetric – different for each of the two DNA strands, and the coding sequences are also asymmetric, the...

Chaetognatha is a minor phylum, comprising transparent marine invertebrates varying in size from 0.5 to 12 cm. The exact phylogenetic position of Chaetognatha in Metazoa has not been deciphered as some embryological characteristics place chaetognaths among deuterostomes and some morphological characteristics place these among protostomes. In this study, the major factors that drive synonymous c...

We have simulated, using Monte Carlo methods, the survival of prokaryotic genes under directional mutational pressure. We have found that the whole pool of genes located on the leading DNA strand differs from that located on the lagging DNA strand and from the subclass of genes coding for ribosomal proteins. The best strategy for most of the non-ribosomal genes is to change the direction of the...

Background: Most of the amino acids are encoded by more than one codon, termed as synonymous codons. Synonymous codon usage is not random as it is unique to species. In each amino acid family, some synonymous codons are preferred and this is referred to as synonymous codon usage bias (SCUB). Trends associated with evolution of SCUB and factors influencing its diversification in plastomes of gen...

Most mutations are deleterious and require energetically costly repairs. Therefore, it seems that any minimization of mutation rate is beneficial. On the other hand, mutations generate genetic diversity indispensable for evolution and adaptation of organisms to changing environmental conditions. Thus, it is expected that a spontaneous mutational pressure should be an optimal compromise between ...