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The Genomic Ecosystem of Transposable Elements in Maize

View ORCID ProfileMichelle C. Stitzer, View ORCID ProfileSarah N. Anderson, View ORCID ProfileNathan M. Springer, View ORCID ProfileJeffrey Ross-Ibarra
doi: https://doi.org/10.1101/559922
Michelle C. Stitzer
1Center for Population Biology and Department of Plant Sciences, University of California, 1 Shields Ave, Davis, CA 95616, USA
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Sarah N. Anderson
2Department of Plant and Microbial Biology, University of Minnesota, Department of Plant and Microbial Biology, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
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Nathan M. Springer
2Department of Plant and Microbial Biology, University of Minnesota, Department of Plant and Microbial Biology, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
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Jeffrey Ross-Ibarra
1Center for Population Biology and Department of Plant Sciences, University of California, 1 Shields Ave, Davis, CA 95616, USA
3Genome Center, University of California, 1 Shields Ave, Davis, CA 95616, USA
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Abstract

Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. But genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level ecological and evolutionary dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between these attributes of the genomic environment and the survival of TE copies and families. Our analyses reveal a diversity of ecological strategies of TE families, each representing the evolution of a distinct ecological niche allowing survival of the TE family. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences generate a rich ecology of the genome, suggesting families of TEs that coexist in time and space compete and cooperate with each other. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity.

‘Lumping our beautiful collection of transposons into a single category is a crime’

-Michael R. Freeling, Mar. 10, 2017

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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 February 28, 2019.
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The Genomic Ecosystem of Transposable Elements in Maize
Michelle C. Stitzer, Sarah N. Anderson, Nathan M. Springer, Jeffrey Ross-Ibarra
bioRxiv 559922; doi: https://doi.org/10.1101/559922
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The Genomic Ecosystem of Transposable Elements in Maize
Michelle C. Stitzer, Sarah N. Anderson, Nathan M. Springer, Jeffrey Ross-Ibarra
bioRxiv 559922; doi: https://doi.org/10.1101/559922

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