Rxivist logo

Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 67,014 bioRxiv papers from 294,953 authors.

Dynamic patterns of transcript abundance of transposable element families in maize

By Sarah N Anderson, Michelle C Stitzer, Peng Zhou, Jeffrey Ross-Ibarra, Cory D. Hirsch, Nathan M Springer

Posted 12 Jun 2019
bioRxiv DOI: 10.1101/668558 (published DOI: 10.1534/g3.119.400431)

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.

Download data

  • Downloaded 367 times
  • Download rankings, all-time:
    • Site-wide: 29,743 out of 67,027
    • In genomics: 2,994 out of 4,553
  • Year to date:
    • Site-wide: 10,569 out of 67,027
  • Since beginning of last month:
    • Site-wide: 22,257 out of 67,027

Altmetric data


Downloads over time

Distribution of downloads per paper, site-wide


Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News