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Dynamic patterns of transcript abundance of transposable element families in maize

View ORCID ProfileSarah N Anderson, View ORCID ProfileMichelle C Stitzer, Peng Zhou, View ORCID ProfileJeffrey Ross-Ibarra, Cory D Hirsch, View ORCID ProfileNathan M Springer
doi: https://doi.org/10.1101/668558
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 Evolution and Ecology and Center for Population Biology, University of California, Davis, California 95616
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Peng Zhou
1Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
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Jeffrey Ross-Ibarra
2Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, California 95616
3Genome Center, University of California, Davis, California 95616
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Cory D Hirsch
4Department of Plant Pathology, 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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  • For correspondence: springer@umn.edu
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Abstract

Transposable Elements (TEs) are mobile elements that contribute the majority of DNA sequences in the maize genome. Due to their repetitive nature, genomic studies of TEs are complicated by the difficulty of properly attributing multi-mapped short reads to specific genomic loci. Here, we utilize a method to attribute RNA-seq reads to TE families rather than particular loci in order to characterize transcript abundance for TE families in the maize genome. We applied this method to assess per-family expression of transposable elements in >800 published RNA-seq libraries representing a range of maize development, genotypes, and hybrids. While a relatively small proportion of TE families are transcribed, expression is highly dynamic with most families exhibiting tissue-specific expression. A large number of TE families were specifically detected in pollen and endosperm, consistent with reproductive dynamics that maintain silencing of TEs in the germ line. We find that B73 transcript abundance is a poor predictor of TE expression in other genotypes and that transcript levels can differ even for shared TEs. Finally, by assessing recombinant inbred line and hybrid transcriptomes, complex patterns of TE transcript abundance across genotypes emerged. Taken together, this study reveals a dynamic contribution of TEs to maize transcriptomes.

Footnotes

  • Email addresses: sna{at}umn.edu, (S.N.A.) mcstitzer{at}ucdavis.edu, (M.C.S.); zhoux379{at}umn.edu, (P.Z.); rossibarra{at}ucdavis.edu, (J.R.I); cdhirsch{at}umn.edu, (C.D.H); springer{at}umn.edu, (N.M.S.)

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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 June 12, 2019.
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Dynamic patterns of transcript abundance of transposable element families in maize
Sarah N Anderson, Michelle C Stitzer, Peng Zhou, Jeffrey Ross-Ibarra, Cory D Hirsch, Nathan M Springer
bioRxiv 668558; doi: https://doi.org/10.1101/668558
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Dynamic patterns of transcript abundance of transposable element families in maize
Sarah N Anderson, Michelle C Stitzer, Peng Zhou, Jeffrey Ross-Ibarra, Cory D Hirsch, Nathan M Springer
bioRxiv 668558; doi: https://doi.org/10.1101/668558

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