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Transposable elements contribute to dynamic genome content in maize

View ORCID ProfileSarah N Anderson, View ORCID ProfileMichelle C Stitzer, View ORCID ProfileAlex B. Brohammer, View ORCID ProfilePeng Zhou, View ORCID ProfileJaclyn M Noshay, View ORCID ProfileCory D. Hirsch, View ORCID ProfileJeffrey Ross-Ibarra, View ORCID ProfileCandice N. Hirsch, View ORCID ProfileNathan M Springer
doi: https://doi.org/10.1101/547398
Sarah N Anderson
1Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
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Michelle C Stitzer
2Department of Plant Sciences and Center for Population Biology, University of California, Davis, California 95616
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Alex B. Brohammer
3Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
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Peng Zhou
1Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
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Jaclyn M Noshay
1Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
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Cory D. Hirsch
4Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
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Jeffrey Ross-Ibarra
2Department of Plant Sciences and Center for Population Biology, University of California, Davis, California 95616
5Genome Center, University of California, Davis, California 95616
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Candice N. Hirsch
3Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
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Nathan M Springer
1Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
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Abstract

Transposable elements (TEs) are ubiquitous components of eukaryotic genomes and can create variation in genomic organization. The majority of maize genomes are composed of TEs. We developed an approach to define shared and variable TE insertions across genome assemblies and applied this method to four maize genomes (B73, W22, Mo17, and PH207). Among these genomes we identified 1.6 Gb of variable TE sequence representing a combination of recent TE movement and deletion of previously existing TEs. Although recent TE movement only accounted for a portion of the TE variability, we identified 4,737 TEs unique to one genome with defined insertion sites in all other genomes. Variable TEs are found for all superfamilies and are distributed across the genome, including in regions of recent shared ancestry among individuals. There are 2,380 genes annotated in the B73 genome located within variable TEs, providing evidence for the role of TEs in contributing to the substantial differences in gene content among these genotypes. The large scope of TE variation present in this limited sample of temperate maize genomes highlights the major contribution of TEs in driving variation in genome organization and gene content.

Significance Statement The majority of the maize genome is comprised of transposable elements (TEs) that have the potential to create genomic variation within species. We developed a method to identify shared and non-shared TEs using whole genome assemblies of four maize inbred lines. Variable TEs are found throughout the maize genome and in comparisons of any two genomes we find ~20% of the genome is due to non-shared TEs. Several thousand maize genes are found within TEs that are variable across lines, highlighting the contribution of TEs to gene content variation. This study creates a comprehensive resource for genomic studies of TE variability among four maize genomes, which will enable studies on the consequences of variable TEs on genome function.

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  • ↵* co-first authors

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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-NC-ND 4.0 International license.
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Posted February 12, 2019.
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Transposable elements contribute to dynamic genome content in maize
Sarah N Anderson, Michelle C Stitzer, Alex B. Brohammer, Peng Zhou, Jaclyn M Noshay, Cory D. Hirsch, Jeffrey Ross-Ibarra, Candice N. Hirsch, Nathan M Springer
bioRxiv 547398; doi: https://doi.org/10.1101/547398
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Transposable elements contribute to dynamic genome content in maize
Sarah N Anderson, Michelle C Stitzer, Alex B. Brohammer, Peng Zhou, Jaclyn M Noshay, Cory D. Hirsch, Jeffrey Ross-Ibarra, Candice N. Hirsch, Nathan M Springer
bioRxiv 547398; doi: https://doi.org/10.1101/547398

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