Abstract

From species to species, and occasionally even between different genes in the same genome, the frequency of G and C nucleotides varies in genomes. In contrast to dicots, monocot grasses have a bimodal distribution of genic GC content. Syntenic genes had significantly higher GC content than non-syntenic genes at their 5'-end in the third position among codons for all 9 species, according to our classification of plant genes from 5 dicots and 4 monocot grasses to related species. Gene duplication is associated with lower GC content because old scattered gene duplications lack synteny to distantly related genomes. Biased GC content can be explained by two mutation types: methylation C to T mutation and gene conversion from A to G. Gene duplication to additional loci is likely to result in non-reciprocal exchanges between homologous alleles, which make it impossible to distinguish when the alleles are identical or heterozygous for presence-absence variation. Gene duplication can result in siRNA synthesis, which can lead to targeted methylation and increase mC-T mutations. Plant genes that have recently been duplicated are more frequently methylated and less likely to go through gene conversion, which together provide a mutational environment that favors AT nucleotides [1]. A subgroup of the syntenic genes in grasses with high GC content has undergone few duplications or has had its duplicate copies eliminated by selection. We put forth the "biased gene duplication / biased mutation" (BDBM) theory as a potential explanation for the genesis and evolution of the duplication-genic GC bias relationship. Empirical evidence for the BDBM model is provided by joint analyses of the genes from 9 angiosperm species, with the genes' duplication status, GC content, methylation levels, and functional classes categorized.