Genome Evolution and GC Patterns Driven By Recombination in Zea mays

Nucleotide bias at the wobble position or the third codon position is a well-documented phenomenon. In Zea mays and other monocots, the GC content in the third codon position of genes (GC3) shows a bimodal distribution. The two defined GC3 peaks in monocots experience divergent evolutionary pressure and differ functionally, with different classes of genes in each peak. High GC3 genes within monocots were categorized into functions involving electron transport or energy pathways, response to stressors and signal transduction.  These observations have been further corroborated in our studies.

Recombination has been perceived to be a driving force for increases in GC3 content. Here we further explore the relationship between recombination and GC content in each of the three codon positions (GC1, GC2, and GC3, collectively termed GCx) by comparing GCx content to motifs underlying double-strand break hotspots and meiocyte-specific gene expression.

Our results indicate a high overlap between high GCx genes of all three categories and genes that contain the double-strand break hotspot motifs. On the other hand, genes that are important in meiosis (early prophase I) are biased against both high GCx genes and genes with the motif, thereby preventing double-strand breaks from occurring in important meiotic genes. The presence of GC and GCx bimodality in maize cannot be fully explained by the wobble hypothesis, suggesting another mechanism for biomodality. As the precursors to gene conversion and sexual recombination, understanding double-strand breaks including their locations and surroundings is critical to understanding process of recombination in entirety.