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Front Plant Sci. 2016 Sep 22;7:1433. eCollection 2016.

Gene Evolutionary Trajectories and GC Patterns Driven by Recombination in Zea mays.

Author information

1
National Center for Genome Resources, Santa Fe NM, USA.
2
Department of Horticultural Science, University of Minnesota, St. Paul MN, USA.
3
Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca NY, USA.
4
Section of Plant Biology, School of Integrative Plant Science, Cornell University, IthacaNY, USA; Biotechnology Resource Center Bioinformatics Facility, Cornell University, IthacaNY, USA.
5
Biotechnology Resource Center Bioinformatics Facility, Cornell University, Ithaca NY, USA.
6
Cereal Disease Laboratory, United States Department of Agriculture - Agricultural Research Service, St. Paul MN, USA.

Abstract

Recombination occurring during meiosis is critical for creating genetic variation and plays an essential role in plant evolution. In addition to creating novel gene combinations, recombination can affect genome structure through altering GC patterns. In maize (Zea mays) and other grasses, another intriguing GC pattern exists. Maize genes show a bimodal GC content distribution that has been attributed to nucleotide bias in the third, or wobble, position of the codon. Recombination may be an underlying driving force given that recombination sites are often associated with high GC content. Here we explore the relationship between recombination and genomic GC patterns by comparing GC gene content at each of the three codon positions (GC1, GC2, and GC3, collectively termed GCx) to instances of a variable GC-rich motif that underlies double strand break (DSB) hotspots and to meiocyte-specific gene expression. Surprisingly, GCx bimodality in maize cannot be fully explained by the codon wobble hypothesis. High GCx genes show a strong overlap with the DSB hotspot motif, possibly providing a mechanism for the high evolutionary rates seen in these genes. On the other hand, genes that are turned on in meiosis (early prophase I) are biased against both high GCx genes and genes with the DSB hotspot motif, possibly allowing important meiotic genes to avoid DSBs. Our data suggests a strong link between the GC-rich motif underlying DSB hotspots and high GCx genes.

KEYWORDS:

GC; codon usage; gene expression; maize; meiocytes; meiosis; recombination; wobble

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