Long-Read cDNA Sequencing Enables a 'Gene-Like' Transcript Annotation of Arabidopsis Transposable Elements

Abstract

High-quality transcript-based annotations of genes facilitates both genome-wide analyses and detailed single locus research. In contrast, transposable element (TE) annotations are rudimentary, consisting of only information on location and type of TE. When analyzing TEs, their repetitiveness and limited annotation prevents the ability to distinguish between potentially functional expressed elements and degraded copies. To improve genome-wide TE bioinformatics, we performed long-read Oxford Nanopore sequencing of cDNAs from Arabidopsis lines deficient in multiple layers of TE repression. We used these uniquely-mapping transcripts to identify the set of TEs able to generate mRNAs, and created a new transcript-based annotation of TEs that we have layered upon the existing high-quality community standard TAIR10 annotation. The improved annotation enables us to test specific standing hypotheses in the TE field. We demonstrate that inefficient TE splicing does not trigger small RNA production, and the cell more strongly targets DNA methylation to TEs that have the potential to make mRNAs. This work provides a transcript-based TE annotation for Arabidopsis, and serves as a blueprint to reduce the genomic complexity associated with repetitive TEs in any organism.