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1

Evolution of eukaryotic chromosomes ? from databases to computer modeling

100%
Mackiewicz D., Waga W., Cebrat S.
Biotechnologia
|
2010
|
issue 4
131-145
EN
Computer simulations of chromosomes' and genomes' evolution suggest that the genes located on relatively large and densely packed chromosomes should be grouped in clusters. Clusters located on homologous chromosomes may complement their defects or they may co-operate providing selective advantage to their hosts. Since recombination inside clusters is harmful, selection leads to the uneven distribution of recombination events along chromosomes - relatively high recombination in the subtelomeric regions and low recombination in the central regions of chromosomes. Uneven distribution of recombinations enables sympatric speciation which can not be predicted by the mean field theories of evolution. Further studies of chromosome evolution require more precise data (the best ? full sequences) of many closely related genomes belonging to the same species.
2

Influence of replication on organization and evolution of bacterial genomes

88%
Kowalczuk M., Mackiewicz D., Mackiewicz P., Polak N., Cebrat S.
Biotechnologia
|
2005
|
issue 3
75-90
EN
In bacterial chromosomes, strong bias in nucleotide composition has been observed between differently replicated DNA strands (leading and lagging ones), and also in many species between the regions proximal and distal to the origin of replication (ori). This bias is also reflected in composition and distribution of genes along the chromosome. Several phenomena connected with the replication of the chromosome are responsible for such polarization, especially mutational pressure, repair mechanisms and recombinations, and also selection pressure. All these phenomena are not indifferent for gene evolution and their rearrangements which are strictly connected with the organization of bacterial chromosome.
3

New insights into phylogeny from genomic point of view

88%
Sobczynski M., Mackiewicz P., Mackiewicz D., Smolarczyk K., Cebrat S.
Biotechnologia
|
2005
|
issue 3
102-117
EN
Availability of fully sequenced genomes contributes to the development of new science named phylogenomics which opens new possibilities of phylogenetic analyses and study of genome evolution based on the whole information coded in genomic DNA. The advantages and disadvantages of the new methods are described. Despite many phenomena such as lineage-specific gene loss, gene duplication and horizontal gene transfer disturbing phylogenetic analyses, the new methods are able to extract some phylogenetic signals in the analysed genomes and construct reliable phylogenetic trees. The genome-based studies support not only the three-domain concept of Tree of Life but they identify previously undetected major clades of prokaryotes as well.
4

High divergence rate of sequences located on different DNA strands in closely related bacterial genomes

76%
Mackiewicz P., Mackiewicz D., Kowalczuk M., Dudkiewicz M., Dudek M. R., Cebrat S.
Journal of Applied Genetics
|
2003
|
vol. 44
|
issue 4
561-584
EN
One of the common features of bacterial genomes is a strong compositional asymmetry between differently replicating DNA strands (leading and lagging). The main cause of the observed bias is the mutational pressure associated with replication. This suggests that genes translocated between differently replicating DNA strands are subjected to a higher mutational pressure, which may influence their composition and divergence rate. Analyses of groups of completely sequenced bacterial genomes have revealed that the highest divergence rate is observed for the DNA sequences that in closely related genomes are located on different DNA strands in respect to their role in replication. Paradoxically, for this group of sequences the absolute values of divergence rate are higher for closely related species than for more diverged ones. Since this effect concerns only the specific group of orthologs, there must be a specific mechanism introducing bias into the structure of chromosome by enriching the set of homologs in trans position in newly diverged species in relatively highly diverged sequences. These highly diverged sequences may be of varied nature: (1) paralogs or other fast-evolving genes under weak selection; or (2) pseudogenes that will probably be eliminated from the genome during further evolution; or (3) genes whose history after divergence is longer than the history of the genomes in which they are found. The use of these highly diverged sequences for phylogenetic analyses may influence the topology and branch length of phylogenetic trees. The changing mutational pressure may contribute to arising of genes with new functions as well.
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