TY - JOUR
T1 - Gene evolutionary trajectories and GC patterns driven by recombination in Zea mays
AU - Sundararajan, Anitha
AU - Dukowic-Schulze, Stefanie
AU - Kwicklis, Madeline
AU - Engstrom, Kayla
AU - Garcia, Nathan
AU - Oviedo, Oliver J.
AU - Ramaraj, Thiruvarangan
AU - Gonzales, Michael D.
AU - He, Yan
AU - Wang, Minghui
AU - Sun, Qi
AU - Pillardy, Jaroslaw
AU - Kianian, Shahryar F.
AU - Pawlowski, Wojciech P.
AU - Chen, Changbin
AU - Mudge, Joann
N1 - 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.
PY - 2016/9/22
Y1 - 2016/9/22
N2 - 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.
AB - 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.
KW - Codon usage
KW - GC
KW - Gene expression
KW - Maize
KW - Meiocytes
KW - Meiosis
KW - Recombination
KW - Wobble
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U2 - 10.3389/fpls.2016.01433
DO - 10.3389/fpls.2016.01433
M3 - Article
AN - SCOPUS:84988624740
SN - 1664-462X
VL - 7
JO - Frontiers in Plant Science
JF - Frontiers in Plant Science
IS - September
M1 - 1433
ER -