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Evidence for co-evolution of gene order and recombination rate

Abstract

There is increasing evidence in eukaryotic genomes that gene order is not random, even allowing for tandem duplication. Notably, in numerous genomes1,2,3,4,5,6, genes of similar expression tend to be clustered. Are there other reasons for clustering of functionally similar genes? If genes are linked to enable genetic, rather than physical clustering, then we also expect that clusters of certain genes might be associated with blocks of reduced recombination rates. Here we show that, in yeast, essential genes are highly clustered and this clustering is independent of clustering of co-expressed genes and of tandem duplications. Adjacent pairs of essential genes are preferentially conserved through evolution. Notably, we also find that clusters of essential genes are in regions of low recombination and that larger clusters have lower recombination rates. These results suggest that selection acts to modify both the fine-scale intragenomic variation in the recombination rate and the distribution of genes and provide evidence for co-evolution of gene order and recombination rate.

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Figure 1: The difference between real and randomized data in the frequencies of blocks of ten genes with x number of essential genes.
Figure 2: The number of occurrences of essential genes having a downstream essential gene y genes away, along the yeast genome.
Figure 3: Sliding-window plot of the number of essential genes (black line) and standard deviation from chromosomal mean recombination rate (gray line) along chromosome 9.
Figure 4: Recombination rate of non-essential genes as a function of the number of essential genes nearby.

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Acknowledgements

We would like to thank F. Kondrashov and B. Papp for comments on an earlier version of the manuscript. C.P is funded by a Royal Society/Nato visiting fellowship and L.D.H. by the UK Biotechnology and Biosciences Research Council.

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Correspondence to Laurence D. Hurst.

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Pál, C., Hurst, L. Evidence for co-evolution of gene order and recombination rate. Nat Genet 33, 392–395 (2003). https://doi.org/10.1038/ng1111

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