Dynamic Patterns of Transcript Abundance of Transposable Element Families in Maize.

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 la

SUBMITTER: Anderson SN 

PROVIDER: S-EPMC6829137 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature