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Recombination and base composition: the case of the highly self-fertilizing plant Arabidopsis thaliana

G Marais1, B Charlesworth1 and S I Wright12*

Author Affiliations

1 Institute of Cell, Animal and Population Biology, University of Edinburgh, EH9 3JT Edinburgh, UK

2 Current address: Department of Biology, York University, 4700 Keele St, Toronto, Ontario M3J 1P3, Canada

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Genome Biology 2004, 5:R45  doi:10.1186/gb-2004-5-7-r45

Published: 14 June 2004



Rates of recombination can vary among genomic regions in eukaryotes, and this is believed to have major effects on their genome organization in terms of base composition, DNA repeat density, intron size, evolutionary rates and gene order. In highly self-fertilizing species such as Arabidopsis thaliana, however, heterozygosity is expected to be strongly reduced and recombination will be much less effective, so that its influence on genome organization should be greatly reduced.


Here we investigated theoretically the joint effects of recombination and self-fertilization on base composition, and tested the predictions with genomic data from the complete A. thaliana genome. We show that, in this species, both codon-usage bias and GC content do not correlate with the local rates of crossing over, in agreement with our theoretical results.


We conclude that levels of inbreeding modulate the effect of recombination on base composition, and possibly other genomic features (for example, transposable element dynamics). We argue that inbreeding should be considered when interpreting patterns of molecular evolution.