Twisted signatures of GC-biased gene conversion embedded in an evolutionary stable karyotype - PubMed (original) (raw)

Twisted signatures of GC-biased gene conversion embedded in an evolutionary stable karyotype

Carina F Mugal et al. Mol Biol Evol. 2013 Jul.

Abstract

The genomes of many vertebrates show a characteristic heterogeneous distribution of GC content, the so-called GC isochore structure. The origin of isochores has been explained via the mechanism of GC-biased gene conversion (gBGC). However, although the isochore structure is declining in many mammalian genomes, the heterogeneity in GC content is being reinforced in the avian genome. Despite this discrepancy, which remains unexplained, examinations of individual substitution frequencies in mammals and birds are both consistent with the gBGC model of isochore evolution. On the other hand, a negative correlation between substitution and recombination rate found in the chicken genome is inconsistent with the gBGC model. It should therefore be important to consider along with gBGC other consequences of recombination on the origin and fate of mutations, as well as to account for relationships between recombination rate and other genomic features. We therefore developed an analytical model to describe the substitution patterns found in the chicken genome, and further investigated the relationships between substitution patterns and several genomic features in a rigorous statistical framework. Our analysis indicates that GC content itself, either directly or indirectly via interrelations to other genomic features, has an impact on the substitution pattern. Further, we suggest that this phenomenon is particularly visible in avian genomes due to their unusually low rate of chromosomal evolution. Because of this, interrelations between GC content and other genomic features are being reinforced, and are as such more pronounced in avian genomes as compared with other vertebrate genomes with a less stable karyotype.

Keywords: GC isochores; base composition; birds; gene conversion; karyotype; recombination.

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Figures

F<sc>ig</sc>. 1.

Fig. 1.

Amount of variation in nucleotide substitution rate explained by the different explanatory variables based on PCR analysis. Left larger panel: PCR analysis of total substitution rate. Right smaller panels: PCR analysis of W → S, S → W, W → W, and S → S nucleotide substitution rates. The height of each bar represents how much of the variance in nucleotide substitution rate is explained by the corresponding PC. The size of each colored area is proportional to the relative contribution of the respective genomic feature within each PC.

F<sc>ig.</sc> 2.

Fig. 2.

Pair-wise relationship between GC* and current GC content. The black solid line represents the linear regression line fitted to the data. The red dashed line represents the bisecting line of the first quadrant (x = y).

F<sc>ig</sc>. 3.

Fig. 3.

Left larger panel: pair-wise relationship between total substitution rate and recombination rate. Right smaller panels: Pair-wise relationship between chicken-specific W → S, S → W, W → W, and S → S nucleotide substitution rate and recombination rate. Correlation coefficients presented in the upper right corner of each panel represent Pearson correlation coefficients. Black lines represent linear regression lines fitted to the data.

F<sc>ig</sc>. 4.

Fig. 4.

Left larger panel: pair-wise relationship between total substitution rate and GC content. Red crosses represent windows where recombination rate estimates are equal to zero and black dots represent windows where recombination rate estimates are larger than zero. Right smaller panels: pair-wise relationship between chicken-specific W → S, S → W, W → W, and S → S nucleotide substitution rate and GC content. Correlation coefficients presented in the upper right corner of each panel represent Pearson correlation coefficients.

F<sc>ig</sc>. 5.

Fig. 5.

Relative difference in W → S and S → W nucleotide substitution rate between chicken and turkey plotted along chicken chromosomes 2 and 4. One dot represents the difference in nucleotide substitution rate estimated for a 1 Mb window at the respective position on the chromosome. The black solid line shows a kernel regression smoother through the point estimates of bandwidth 5. The vertical red dashed line in each panel indicates the fission point of chromosome 2 or the fusion point of chromosome 4, which occurred in the turkey and chicken lineage, respectively, after their divergence.

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