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Adaptation in plant genomes: bigger is different

View ORCID ProfileWenbin Mei, View ORCID ProfileMarkus G Stetter, View ORCID ProfileDaniel J Gates, View ORCID ProfileMichelle C Stitzer, View ORCID ProfileJeffrey Ross-Ibarra
doi: https://doi.org/10.1101/196501
Wenbin Mei
1Dept. of Plant Sciences, University of California, Davis, CA 95616
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Markus G Stetter
1Dept. of Plant Sciences, University of California, Davis, CA 95616
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Daniel J Gates
1Dept. of Plant Sciences, University of California, Davis, CA 95616
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Michelle C Stitzer
1Dept. of Plant Sciences, University of California, Davis, CA 95616
2Center for Population Biology, University of California, Davis, CA 95616
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Jeffrey Ross-Ibarra
1Dept. of Plant Sciences, University of California, Davis, CA 95616
2Center for Population Biology, University of California, Davis, CA 95616
3Genome Center, University of California, Davis, CA 95616
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Abstract

Here we have proposed the functional space hypothesis, positing that mutational target size scales with genome size, impacting the number, source, and genomic location of beneficial mutations that contribute to adaptation. Though motivated by preliminary evidence, mostly from Arabidopsis and maize, more data are needed before any rigorous assessment of the hypothesis can be made. If correct, the functional space hypothesis suggests that we should expect plants with large genomes to exhibit more functional mutations outside of genes, more regulatory variation, and likely less signal of strong selective sweeps reducing diversity. These differences have implications for how we study the evolution and development of plant genomes, from where we should look for signals of adaptation to what patterns we expect adaptation to leave in genetic diversity or gene expression data. While flowering plant genomes vary across more than three orders of magnitude in size, most studies of both functional and evolutionary genomics have focused on species at the extreme small edge of this scale. Our hypothesis predicts that methods and results from these small genomes may not replicate well as we begin to explore large plant genomes. Finally, while we have focused here on evidence from plant genomes, we see no a priori reason why similar arguments might not hold in other taxa as well.

Footnotes

  • ↵* rossibarra{at}ucdavis.edu

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted October 10, 2017.
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Adaptation in plant genomes: bigger is different
Wenbin Mei, Markus G Stetter, Daniel J Gates, Michelle C Stitzer, Jeffrey Ross-Ibarra
bioRxiv 196501; doi: https://doi.org/10.1101/196501
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Adaptation in plant genomes: bigger is different
Wenbin Mei, Markus G Stetter, Daniel J Gates, Michelle C Stitzer, Jeffrey Ross-Ibarra
bioRxiv 196501; doi: https://doi.org/10.1101/196501

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