Gene evolutionary trajectories and GC patterns driven by recombination in Zea mays

Anitha Sundararajan, Stefanie Dukowic-Schulze, Madeline Kwicklis, Kayla Engstrom, Nathan Garcia, Oliver J. Oviedo, Thiruvarangan Ramaraj, Michael D. Gonzales, Yan He, Minghui Wang, Qi Sun, Jaroslaw Pillardy, Shahryar F. Kianian, Wojciech P. Pawlowski, Changbin Chen, Joann Mudge

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


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.

Original languageEnglish (US)
Article number1433
JournalFrontiers in Plant Science
Issue numberSeptember
StatePublished - Sep 22 2016

Bibliographical note

Funding Information:
This research was supported by the United States National Science Foundation grant IOS-1025881 and by an Institutional Development Award(IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number P20GM103451.

Publisher Copyright:
© 2016 Sundararajan, Dukowic-Schulze, Kwicklis, Engstrom, Garcia, Oviedo, Ramaraj, Gonzales, He, Wang, Sun, Pillardy, Kianian, Pawlowski, Chen and Mudge.


  • Codon usage
  • GC
  • Gene expression
  • Maize
  • Meiocytes
  • Meiosis
  • Recombination
  • Wobble


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