Genome analyses and modelling the relationships between coding density, recombination rate and chromosome length

Abstract

This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting galley proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. To whom correspondence should be addressed. E-mail: dorota@smorfland.uni.wroc.pl AbstractIn the human genomes, recombination frequency between homologous chromosomes during meiosis is highly correlated with their physical length while it differs significantly when their coding density is considered. Furthermore, it has been observed that the recombination events are distributed unevenly along the chromosomes. We have found that many of such recombination properties can be predicted by computer simulations of population evolution based on the Monte Carlo methods. For example, these simulations have shown that the probability of acceptance of the recombination events by selection is higher at the ends of chromosomes and lower in their middle parts. The regions of high coding density are more prone to enter the strategy of haplotype complementation and to form clusters of genes which are "recombination deserts". The phenomenon of switching in-between the purifying selection and haplotype complementation has a phase transition character, and many relations between the effective population size, coding density, chromosome size and recombination frequency are those of the power law type.2

Distribution of Recombination Hotspots in the Human Genome – A Comparison of Computer Simulations with Real Data

“…Such a preferential placement of the linked genes in the centre of chromosome suppresses recombination in this region that may influence the global distribution of recombination hotspots observed in human chromosomes. This is in agreement with the view that humans have evolved in relatively small populations [39], [52], in which the formation of linked genes is preferred [38]–[40], [51]. If we consider this problem from the point of evolutionary costs, it seems that avoiding recombination in a region of linked genes is more effective than elimination of recombinants from the population [38], [53].…”

“…These groups of genes consisted mainly of heterozygous loci that could complement their defects with other corresponding haplotypes present in the population. Therefore, when these groups became established by selection, any recombinations breaking these haplotypes had a deleterious effect and were selected against [38], [39]. Such groups of linked genes were not formed at the ends of chromosomes where purifying selection associated with a high recombination rate dominated.…”

The Role of Haplotype Complementation and Purifying Selection in the Genome Evolution

“…The smallest human chromosome (excluding Y chromosome) contains 280 genes while the largest one about 2200 genes. On the other hand genetic length of the shortest one is 62cM while of the largest chromosome is 278cM (for details see International HapMap Consortium 2005 and [22]). Since the correlation between coding capacity and recombination rate is not very high in the human genome ( Fig.11) -our natural chromosomes may differ significantly in relations between recombination rate and number of genes.…”

Bioinformatics and Computational Biology in Poland

“…At the Faculty of Biology and Animal Science of the Wrocław University of Environmental and Life Sciences, Joanna Szyda's group works on statistic genomics of animals [82]. Stanisław Cebrat's group at the Faculty of Biotechnology of the University of Wrocław is working in the area of theoretical and computational genomics, e.g., on Monte Carlo simulations of genome and population evolution [26], [83].…”